Thread: [Apbs-users] Using parameters other than those defined in APBS
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From: Zu T. Y. <ye...@in...> - 2006-07-18 14:30:39
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Hi, I would just like to ask about the procedures needed to read in parameters not defined in the forcefield used to assign radii and charges. If I want to add in the new parameters for the new residues types, can I just to so to the bottom of the AMBER.dat? Do I need to change AMBER.names...I noticed that it has lines which specified the residue names.....can I just add similar lines, but with the new residue name below? PDB2PQR will omit residues/atoms that do not match those in the forcefield, is there an option that can be specified to stop that? Or how do I use pdb2pqr in conjuction with the "read Parm" command (with a parm file just specifying the new residue)? Many Thanks for any help/advice! ZT |
From: Todd D. <to...@cc...> - 2006-07-18 14:45:18
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Hello - I'm going to CC the pdb2pqr-users mailing list, since this is more of a PDB2PQR question. If you would simply like to add parameters to a forcefield, then all you need to do is append to the bottom of the *.dat file (in this case AMBER.DAT). The *.names file is used when the atom/residue names in the PDB file do not match those in the *.dat file, so as long as you name everything appropriately you won't have to worry about that. Right now there's no way to "turn off" PDB2PQR's behavior of omitting atoms it doesn't recognize - the logic behind this is that if the parameters are not present, the rationale for including it in a PQR is rather diminished as nothing would have changed from the PDB file. You can always add the missing parameters as mentioned above, or if you just want the atoms present you can copy them over from the PDB file. As for using the "read parm" command, for the most part this has been deprecated in favor of PDB2PQR. Your best solution (assuming you know the parameters) is to add them to the *.DAT file. Please see both the PDB2PQR user guide (http://pdb2pqr.sourceforge.net/userguide.html#userff) and the README in the pdb2pqr/examples/1a1p/ directory for more helpful info on adding to forcefields. Todd On 7/18/06, Zu Thur Yew <ye...@in...> wrote: > Hi, > > I would just like to ask about the procedures needed to read in > parameters not defined in the forcefield used to assign radii and charges. > > If I want to add in the new parameters for the new residues types, can I > just to so to the bottom of the AMBER.dat? Do I need to change > AMBER.names...I noticed that it has lines which specified the residue > names.....can I just add similar lines, but with the new residue name below? > > PDB2PQR will omit residues/atoms that do not match those in the > forcefield, is there an option that can be specified to stop that? Or > how do I use pdb2pqr in conjuction with the "read Parm" command (with a > parm file just specifying the new residue)? > > Many Thanks for any help/advice! > > ZT > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys -- and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > |