TER characters between residues in exported PDB ?
Hello all, I would like to know if there is any way how to export from Chimera molecular structure in PDB format but with TER string between all residues in the file. This would be very helpful if one prepares in Chimera PDB inputs (containing also non protein or non DNA/RNA molecules) for Amber because Amber (Leap) automatically tries to create bonds between all consecutive residues unless they are separated by TER string. Thank you very much for any useful information. Best wishes, Marek -- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
Hi Marek, If you are going to use Amber, might as well just use Write Prmtop instead (in menu under Tools... Amber): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addions/writeprmtop.html> This saves both a prmtop file and a inpcrd file. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 7, 2012, at 11:19 AM, Marek Maly wrote:
Hello all,
I would like to know if there is any way how to export from Chimera molecular structure in PDB format but with TER string between all residues in the file.
This would be very helpful if one prepares in Chimera PDB inputs (containing also non protein or non DNA/RNA molecules) for Amber because Amber (Leap) automatically tries to create bonds between all consecutive residues unless they are separated by TER string.
Thank you very much for any useful information.
Best wishes,
Marek
I forgot to mention: very recently we updated to AmberTools 12, so if you want the latest recommended force field (ff12SB), please get a new daily build. <http://www.cgl.ucsf.edu/chimera/download.html#daily> Elaine On Jun 7, 2012, at 12:12 PM, Elaine Meng wrote:
Hi Marek, If you are going to use Amber, might as well just use Write Prmtop instead (in menu under Tools... Amber): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addions/writeprmtop.html>
This saves both a prmtop file and a inpcrd file. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 7, 2012, at 11:19 AM, Marek Maly wrote:
Hello all,
I would like to know if there is any way how to export from Chimera molecular structure in PDB format but with TER string between all residues in the file.
This would be very helpful if one prepares in Chimera PDB inputs (containing also non protein or non DNA/RNA molecules) for Amber because Amber (Leap) automatically tries to create bonds between all consecutive residues unless they are separated by TER string.
Thank you very much for any useful information.
Best wishes,
Marek
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Thanks ! I'll take a look on it. Best wishes, Marek Dne Thu, 07 Jun 2012 22:07:16 +0200 Elaine Meng <meng@cgl.ucsf.edu> napsal/-a:
I forgot to mention: very recently we updated to AmberTools 12, so if you want the latest recommended force field (ff12SB), please get a new daily build.
<http://www.cgl.ucsf.edu/chimera/download.html#daily>
Elaine
On Jun 7, 2012, at 12:12 PM, Elaine Meng wrote:
Hi Marek, If you are going to use Amber, might as well just use Write Prmtop instead (in menu under Tools... Amber): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addions/writeprmtop.html>
This saves both a prmtop file and a inpcrd file. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 7, 2012, at 11:19 AM, Marek Maly wrote:
Hello all,
I would like to know if there is any way how to export from Chimera molecular structure in PDB format but with TER string between all residues in the file.
This would be very helpful if one prepares in Chimera PDB inputs (containing also non protein or non DNA/RNA molecules) for Amber because Amber (Leap) automatically tries to create bonds between all consecutive residues unless they are separated by TER string.
Thank you very much for any useful information.
Best wishes,
Marek
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Dear Elaine, thanks for your prompt information ! Unfortunately systems which I am simulating are not so simple usually are composed of several parts for which different ff should be used e.g. example system = branched polymer (gaff) + DNA (ff99bsc0) or branched polymer (gaff) + sugar (GLYCAM) + peptide (ff99SB) etc. I am not sure if actual implementation of Amber/Antechamber module in Chimera can manage such nontrivial systems. Another thing I have already for my GAFF-param molecules "prepin" and "frcmod" files (wider library for different molecular segments). Is Chimera somehow able to accept them when creating prmtop and incprd files of the given system ? I think that to add into "Save PDB" dialog just one more option ("Separate residues by TERs") should be easy work but very valuable for guys like me, otherwise we have to use own post-processing which takes some additional time. I noticed also another thing which creates a small troubles. If I load in Chimera system AB then delete in Chimera part B and save the rest (part A) as the PDB file there still remain CONECT records which belongs to deleted atoms B. If there is no important reason for this, might be this also corrected as there are again problems in Amber ("Illegal CONECT record in pdb file") in that case so one have to correct it manually each time. Thank you very much in advance ! Best wishes, Marek Dne Thu, 07 Jun 2012 21:12:10 +0200 Elaine Meng <meng@cgl.ucsf.edu> napsal/-a:
Hi Marek, If you are going to use Amber, might as well just use Write Prmtop instead (in menu under Tools... Amber): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addions/writeprmtop.html>
This saves both a prmtop file and a inpcrd file. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 7, 2012, at 11:19 AM, Marek Maly wrote:
Hello all,
I would like to know if there is any way how to export from Chimera molecular structure in PDB format but with TER string between all residues in the file.
This would be very helpful if one prepares in Chimera PDB inputs (containing also non protein or non DNA/RNA molecules) for Amber because Amber (Leap) automatically tries to create bonds between all consecutive residues unless they are separated by TER string.
Thank you very much for any useful information.
Best wishes,
Marek
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Hi Marek, Chimera will use gaff for nonstandard residues and your chosen force field for standard residues, but it does not know about carbohydrates and GLYCAM. I believe it would lump them with the other nonstandard residues (use gaff/Antechamber). I don't think there is any way to tell Chimera to also use your own frcmod files. Also, in the current daily build, ff12SB is recommended and ff99* deprecated (has been removed from the Add Charge GUI, although still available in the addcharge command). There is some discussion in the Ambertools12 manual about why the ff99* versions are deprecated. Best, Elaine On Jun 7, 2012, at 1:12 PM, Marek Maly wrote:
Dear Elaine,
thanks for your prompt information !
Unfortunately systems which I am simulating are not so simple usually are composed of several parts for which different ff should be used e.g.
example system = branched polymer (gaff) + DNA (ff99bsc0)
or
branched polymer (gaff) + sugar (GLYCAM) + peptide (ff99SB)
etc.
I am not sure if actual implementation of Amber/Antechamber module in Chimera can manage such nontrivial systems.
Another thing I have already for my GAFF-param molecules "prepin" and "frcmod" files (wider library for different molecular segments). Is Chimera somehow able to accept them when creating prmtop and incprd files of the given system ?
I think that to add into "Save PDB" dialog just one more option ("Separate residues by TERs") should be easy work but very valuable for guys like me, otherwise we have to use own post-processing which takes some additional time.
I noticed also another thing which creates a small troubles. If I load in Chimera system AB then delete in Chimera part B and save the rest (part A) as the PDB file there still remain CONECT records which belongs to deleted atoms B. If there is no important reason for this, might be this also corrected as there are again problems in Amber ("Illegal CONECT record in pdb file") in that case so one have to correct it manually each time.
Thank you very much in advance !
Best wishes,
Marek
Dne Thu, 07 Jun 2012 21:12:10 +0200 Elaine Meng <meng@cgl.ucsf.edu> napsal/-a:
Hi Marek, If you are going to use Amber, might as well just use Write Prmtop instead (in menu under Tools... Amber): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addions/writeprmtop.html>
This saves both a prmtop file and a inpcrd file. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 7, 2012, at 11:19 AM, Marek Maly wrote:
Hello all,
I would like to know if there is any way how to export from Chimera molecular structure in PDB format but with TER string between all residues in the file.
This would be very helpful if one prepares in Chimera PDB inputs (containing also non protein or non DNA/RNA molecules) for Amber because Amber (Leap) automatically tries to create bonds between all consecutive residues unless they are separated by TER string.
Thank you very much for any useful information.
Best wishes,
Marek
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-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Yes I see, but these are the reasons: (actually absent of GAFF, impossiblity to use more specialized ff like GLYCAM, impossibility to use contributed libraries (e.g. for metaloproteines), impossibility to use already created prepin/frcmod files, impossibility to use ff mixtures) why in such a complicated systems one have to proceed by the classical way i.e. direct using of Antechamber in Amber. I also found (in actual alpha version) just possibility to save PRMTOP file but both input files: PRMTOP (ff parameters) and INPCRD (atom coordinates) are necessary to start simulation in Amber. So again I (and perhaps not only me) would be very grateful for adding that new small but very useful TER feature and eventually that correction of CONECT records as I described below. Thanks again ! Best wishes, Marek Dne Thu, 07 Jun 2012 22:25:56 +0200 Elaine Meng <meng@cgl.ucsf.edu> napsal/-a:
Hi Marek, Chimera will use gaff for nonstandard residues and your chosen force field for standard residues, but it does not know about carbohydrates and GLYCAM. I believe it would lump them with the other nonstandard residues (use gaff/Antechamber).
I don't think there is any way to tell Chimera to also use your own frcmod files.
Also, in the current daily build, ff12SB is recommended and ff99* deprecated (has been removed from the Add Charge GUI, although still available in the addcharge command). There is some discussion in the Ambertools12 manual about why the ff99* versions are deprecated. Best, Elaine
On Jun 7, 2012, at 1:12 PM, Marek Maly wrote:
Dear Elaine,
thanks for your prompt information !
Unfortunately systems which I am simulating are not so simple usually are composed of several parts for which different ff should be used e.g.
example system = branched polymer (gaff) + DNA (ff99bsc0)
or
branched polymer (gaff) + sugar (GLYCAM) + peptide (ff99SB)
etc.
I am not sure if actual implementation of Amber/Antechamber module in Chimera can manage such nontrivial systems.
Another thing I have already for my GAFF-param molecules "prepin" and "frcmod" files (wider library for different molecular segments). Is Chimera somehow able to accept them when creating prmtop and incprd files of the given system ?
I think that to add into "Save PDB" dialog just one more option ("Separate residues by TERs") should be easy work but very valuable for guys like me, otherwise we have to use own post-processing which takes some additional time.
I noticed also another thing which creates a small troubles. If I load in Chimera system AB then delete in Chimera part B and save the rest (part A) as the PDB file there still remain CONECT records which belongs to deleted atoms B. If there is no important reason for this, might be this also corrected as there are again problems in Amber ("Illegal CONECT record in pdb file") in that case so one have to correct it manually each time.
Thank you very much in advance !
Best wishes,
Marek
Dne Thu, 07 Jun 2012 21:12:10 +0200 Elaine Meng <meng@cgl.ucsf.edu> napsal/-a:
Hi Marek, If you are going to use Amber, might as well just use Write Prmtop instead (in menu under Tools... Amber): <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addions/writeprmtop.html>
This saves both a prmtop file and a inpcrd file. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 7, 2012, at 11:19 AM, Marek Maly wrote:
Hello all,
I would like to know if there is any way how to export from Chimera molecular structure in PDB format but with TER string between all residues in the file.
This would be very helpful if one prepares in Chimera PDB inputs (containing also non protein or non DNA/RNA molecules) for Amber because Amber (Leap) automatically tries to create bonds between all consecutive residues unless they are separated by TER string.
Thank you very much for any useful information.
Best wishes,
Marek
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Tuto zpravu proveril ESET NOD32 Antivirus.
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/ _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Tuto zpravu proveril ESET NOD32 Antivirus.
-- Tato zpráva byla vytvořena převratným poštovním klientem Opery: http://www.opera.com/mail/
Hi Marek, On Jun 7, 2012, at 1:48 PM, Marek Maly wrote:
I also found (in actual alpha version) just possibility to save PRMTOP file but both input files: PRMTOP (ff parameters) and INPCRD (atom coordinates) are necessary to start simulation in Amber.
This doesn't solve the other issues, but I thought I should mention that Write Prmtop saves both prmtop and inpcrd using the filename you give it. Elaine
OK, I just saw in my short look in given Chimera dialog that there is written only "File type: Prmtop" so that a bit confused me... Thanks, Best wishes, Marek Dne Thu, 07 Jun 2012 22:53:38 +0200 Elaine Meng <meng@cgl.ucsf.edu> napsal/-a:
Hi Marek,
On Jun 7, 2012, at 1:48 PM, Marek Maly wrote:
I also found (in actual alpha version) just possibility to save PRMTOP file but both input files: PRMTOP (ff parameters) and INPCRD (atom coordinates) are necessary to start simulation in Amber.
This doesn't solve the other issues, but I thought I should mention that Write Prmtop saves both prmtop and inpcrd using the filename you give it.
Elaine __________ Informace od ESET NOD32 Antivirus, verze databaze 7204 (20120607) __________
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On Jun 7, 2012, at 1:12 PM, Marek Maly wrote:
Another thing I have already for my GAFF-param molecules "prepin" and "frcmod" files (wider library for different molecular segments). Is Chimera somehow able to accept them when creating prmtop and incprd files of the given system ?
Hi Marek, Allowing WritePrmtop to accept custom leaprc files is on my to-do list but it just hasn't happened yet. I'll add you to the feature- request ticket in the Chimera Trac database so you'll know when it gets implemented. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jun 7, 2012, at 1:12 PM, Marek Maly wrote:
If I load in Chimera system AB then delete in Chimera part B and save the rest (part A) as the PDB file there still remain CONECT records which belongs to deleted atoms B
Hi Marek, Can you provide an example for me where this occurs? In my tests this did not happen, so I need some help reproducing this. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jun 7, 2012, at 11:19 AM, Marek Maly wrote:
Amber (Leap) automatically tries to create bonds between all consecutive residues unless they are separated by TER string.
Hi Marek, So you're saying that if you take a completely standard PDB entry from the RCSB that has water in it, and read that into Leap, Leap will connect all the waters in a chain? Wouldn't it be better to ask on the Amber list to have that behavior corrected so that all Amber users could benefit from it? Anyway, you can work around the issue in Chimera by forcing Chimera to believe that all the residues in your structure are standard non- HET residues. It will then write them out in ATOM records and place TER cards between them when they're not connected. Run this Python script (save to a file ending with .py and open it with the "open" command or File->Open) with your structure open: from chimera import Molecule, openModels, PDBio for m in openModels.list(modelTypes=[Molecule]): for r in m.residues: r.isHet = False PDBio.addStandardResidue(r.type) Then simply save your PDB file. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
participants (3)
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Elaine Meng -
Eric Pettersen -
Marek Maly