Hi all, Does anyone knows any alternative charge calculating software packages to PDB2PQR. I need to calculate partial charge distribution but the local copy of PDB2PQR that I installed has some kind of glitch where it is scrapping all of the water molecules from my solvated protein while doing the analysis. I think it has something to do with the side of my PDB file since I am using about 30K atoms, at least, and everything goes perfectly when I work with less 10K atoms. So, I guess the second question is, has anyone else ever encountered this problem? Sincerely, Nikolay Rodionov
Hi Nikolay, Well, Chimera itself does charge assignments, see the Add Charge tool (in Chimera menu under Tools... Structure Editing). It uses a lookup table for standard residues and Antechamber to calculate charges for other residues, as explained in the manual page: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge...> However, Chimera does not write out the PQR format, it only reads it. I can't answer anything specific about the PDB2PQR server...it's not part of Chimera and I haven't used it very much. I hope this helps, 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 Apr 20, 2012, at 7:53 AM, Nikolay Igorovich Rodionov wrote:
Hi all, Does anyone knows any alternative charge calculating software packages to PDB2PQR. I need to calculate partial charge distribution but the local copy of PDB2PQR that I installed has some kind of glitch where it is scrapping all of the water molecules from my solvated protein while doing the analysis. I think it has something to do with the side of my PDB file since I am using about 30K atoms, at least, and everything goes perfectly when I work with less 10K atoms. So, I guess the second question is, has anyone else ever encountered this problem? Sincerely, Nikolay Rodionov
Does chimera allow you to define the force-field? I'm concentrating on using PARSE for most of my work. Also, I like how PDB2PQR uses proPKA as the model for predicting pKa values in the charge calculation. Does Chimera share this functionality? Thank you, Nikolay Rodionov -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, April 20, 2012 9:13 AM To: Nikolay Igorovich Rodionov Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Charge calculations PDB2PQR Hi Nikolay, Well, Chimera itself does charge assignments, see the Add Charge tool (in Chimera menu under Tools... Structure Editing). It uses a lookup table for standard residues and Antechamber to calculate charges for other residues, as explained in the manual page: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge...> However, Chimera does not write out the PQR format, it only reads it. I can't answer anything specific about the PDB2PQR server...it's not part of Chimera and I haven't used it very much. I hope this helps, 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 Apr 20, 2012, at 7:53 AM, Nikolay Igorovich Rodionov wrote:
Hi all, Does anyone knows any alternative charge calculating software packages to PDB2PQR. I need to calculate partial charge distribution but the local copy of PDB2PQR that I installed has some kind of glitch where it is scrapping all of the water molecules from my solvated protein while doing the analysis. I think it has something to do with the side of my PDB file since I am using about 30K atoms, at least, and everything goes perfectly when I work with less 10K atoms. So, I guess the second question is, has anyone else ever encountered this problem? Sincerely, Nikolay Rodionov
Hi Nikolay, The choices of force field are listed in the Add Charge manual page, but they are all versions from Amber: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge...> Before charges are added, the user is prompted to add hydrogens with the AddH tool. There is no choice of pH, sidechains are given their probable state near pH 7 (except histidine is determined by local environment, by default), but the user can control specific sidechains' protonation state as desired, as explained in the AddH manual page: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html> So Chimera does not provide PARSE charges, and does not do pKa prediction. However, if you created an attribute definition file containing the PARSE charges (which could be a lot of work), you could use it to assign "custom" charges in Chimera. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...> Also, you could run propKa yourself and then during hydrogen addition in Chimera, specify the protonation states individually to agree with propKa's predictions. Probably more steps than you had in mind, and again, Chimera doesn't output PQR format. Elaine On Apr 20, 2012, at 9:17 AM, Nikolay Igorovich Rodionov wrote:
Does chimera allow you to define the force-field? I'm concentrating on using PARSE for most of my work. Also, I like how PDB2PQR uses proPKA as the model for predicting pKa values in the charge calculation. Does Chimera share this functionality? Thank you, Nikolay Rodionov
Hi, I'm actually working on interfacing Chimera with the pdb2pqr web service at NBCR. I have something that works for a couple simple PDB entries. Would it be possible for me to get your data for testing? If it works, the new tool should be in the Chimera daily builds by next week. Conrad On 4/20/2012 7:53 AM, Nikolay Igorovich Rodionov wrote:
Hi all,
Does anyone knows any alternative charge calculating software packages to PDB2PQR. I need to calculate partial charge distribution but the local copy of PDB2PQR that I installed has some kind of glitch where it is scrapping all of the water molecules from my solvated protein while doing the analysis. I think it has something to do with the side of my PDB file since I am using about 30K atoms, at least, and everything goes perfectly when I work with less 10K atoms. So, I guess the second question is, has anyone else ever encountered this problem?
Sincerely,
Nikolay Rodionov
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I avoided the larger issues in my previous reply, trying to stick to Chimera information, but I suppose it needs to be said: Since the PDB2PQR server is primarily for preparing structures for continuum electrostatics calculations, it only makes sense (to me) that it would remove all the water molecules. I.e. these calculations are normally done without explicit waters; solvent is instead modeled as a high-dielectric continuum. Perhaps Nikolay should ask the APBS and/or PDB2PQR people, if he wants a more direct discussion of whether his water molecules should be retained. Best, Elaine On Apr 20, 2012, at 9:44 AM, Conrad Huang wrote:
Hi,
I'm actually working on interfacing Chimera with the pdb2pqr web service at NBCR. I have something that works for a couple simple PDB entries. Would it be possible for me to get your data for testing? If it works, the new tool should be in the Chimera daily builds by next week.
Conrad
On 4/20/2012 7:53 AM, Nikolay Igorovich Rodionov wrote:
Hi all,
Does anyone knows any alternative charge calculating software packages to PDB2PQR. I need to calculate partial charge distribution but the local copy of PDB2PQR that I installed has some kind of glitch where it is scrapping all of the water molecules from my solvated protein while doing the analysis. I think it has something to do with the side of my PDB file since I am using about 30K atoms, at least, and everything goes perfectly when I work with less 10K atoms. So, I guess the second question is, has anyone else ever encountered this problem?
Sincerely,
Nikolay Rodionov
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I've actually been talking with the developers of PDB2PQR about the problem and they've said that they that waters should be retained. One of the reasons I have been using PDB2PQR is that it optimizes hydrogen bonding and repositions waters accordingly, which gives me a sense of where hydrogen bonding between waters and protein occur. I should have asked about this in my previous email, does chimera optimize hydrogen bonds? Nikolay Rodionov -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, April 20, 2012 9:52 AM To: Conrad Huang Cc: Nikolay Igorovich Rodionov; chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Charge calculations PDB2PQR I avoided the larger issues in my previous reply, trying to stick to Chimera information, but I suppose it needs to be said: Since the PDB2PQR server is primarily for preparing structures for continuum electrostatics calculations, it only makes sense (to me) that it would remove all the water molecules. I.e. these calculations are normally done without explicit waters; solvent is instead modeled as a high-dielectric continuum. Perhaps Nikolay should ask the APBS and/or PDB2PQR people, if he wants a more direct discussion of whether his water molecules should be retained. Best, Elaine On Apr 20, 2012, at 9:44 AM, Conrad Huang wrote:
Hi,
I'm actually working on interfacing Chimera with the pdb2pqr web service at NBCR. I have something that works for a couple simple PDB entries. Would it be possible for me to get your data for testing? If it works, the new tool should be in the Chimera daily builds by next week.
Conrad
On 4/20/2012 7:53 AM, Nikolay Igorovich Rodionov wrote:
Hi all,
Does anyone knows any alternative charge calculating software packages to PDB2PQR. I need to calculate partial charge distribution but the local copy of PDB2PQR that I installed has some kind of glitch where it is scrapping all of the water molecules from my solvated protein while doing the analysis. I think it has something to do with the side of my PDB file since I am using about 30K atoms, at least, and everything goes perfectly when I work with less 10K atoms. So, I guess the second question is, has anyone else ever encountered this problem?
Sincerely,
Nikolay Rodionov
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Nikolay, Chimera has a Minimize Structure tool (in menu under Tools... Structure Editing). <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.h...> It is just a local minimization using the Amber force field (choices discussed previously), but you could try it and see if the amount of repositioning is sufficient for your purposes. The H-bonds are not explicitly optimized but the force field will tend to improve H-bonds, especially in nonfrustrated systems. For example, here is a little video of improving H-bonds while minimizing a box of water here: <http://www.cgl.ucsf.edu/chimera/data/movie-howto-mar2012/movie_examples.html...> One possibility would be to freeze the protein atoms (move only the waters) during minimization. Best, Elaine On Apr 20, 2012, at 9:57 AM, Nikolay Igorovich Rodionov wrote:
I've actually been talking with the developers of PDB2PQR about the problem and they've said that they that waters should be retained. One of the reasons I have been using PDB2PQR is that it optimizes hydrogen bonding and repositions waters accordingly, which gives me a sense of where hydrogen bonding between waters and protein occur. I should have asked about this in my previous email, does chimera optimize hydrogen bonds?
Nikolay Rodionov
participants (3)
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Conrad Huang -
Elaine Meng -
Nikolay Igorovich Rodionov