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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