Thread: [Apbs-users] Problem with hydrogens while adding a residue to a force field
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From: Miguel O. L. <mol...@ya...> - 2007-04-30 11:06:26
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, (Sorry for cross-posting with pdb2pqr, but I didn't get any answer from there) I'm using pdb2pqr version 1.1.2, and have now also tried now with 1.2.1 I have added a new residue (a modified lysine) to the CHARMM.DAT force-field data, in fact making a copy to CHARMM_LYR.DAT. I have also copied CHARMM.names to CHARMM_LYR.names without further editing. This a lysine bound to retinal, that I call LYR. I have introduced all the hydrogens with charges, radii and epsilon (or atom type for the 1.2.1 version). However, when I run: pdb2pqr --ff=CHARMM_LYR file.pdb file.pqr the hydrogens are not added to the LYR residue and hence its total charge is wrong and fractional. I must be missing something... I suppose I should be telling how the hydrogens are added and how this modified amino-acid gets connected to the rest of the protein, but I couldn't find how to do it. I would appreciate if you can give me a reference or the relevant part of the manual from where I could find out how to solve this problem. Thanking you in advance for your help, Miguel - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: mol...@ya... www: http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) iD8DBQFGNc3JF6oOrDvhbQIRAuc0AJ9f3sbpT5pxRvGCPF+T3nSfRNa6WQCeN5pW 4xyC1vp6uezlnfa6kS0dzmU= =6pvr -----END PGP SIGNATURE----- |
From: Todd D. <to...@cc...> - 2007-04-30 13:26:35
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Hi Miguel - Modifying the DAT file, as you can probably tell, will only let PDB2PQR know how to assign charges to already existing atoms, not rebuild missing hydrogens. You may want to play around with adding the custom LYR residue (using LYS as a model) to the AA.xml file - this has a reference coordinate set which will potentially allow you to rebuild hydrogens accordingly. This is somewhat outside the scope of what's currently supported (I haven't tested how well it works), but in theory you should be able to force PDB2PQR to add hydrogens this way. Todd On 4/30/07, Miguel Ortiz Lombardia <mol...@ya...> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Dear all, > > (Sorry for cross-posting with pdb2pqr, but I didn't get any answer from > there) > > I'm using pdb2pqr version 1.1.2, and have now also tried now with 1.2.1 > > I have added a new residue (a modified lysine) to the CHARMM.DAT > force-field data, in fact making a copy to CHARMM_LYR.DAT. I have also > copied CHARMM.names to CHARMM_LYR.names without further editing. This a > lysine bound to retinal, that I call LYR. I have introduced all the > hydrogens with charges, radii and epsilon (or atom type for the 1.2.1 > version). However, when I run: > > pdb2pqr --ff=3DCHARMM_LYR file.pdb file.pqr > > the hydrogens are not added to the LYR residue and hence its total > charge is wrong and fractional. > > I must be missing something... I suppose I should be telling how the > hydrogens are added and how this modified amino-acid gets connected to > the rest of the protein, but I couldn't find how to do it. I would > appreciate if you can give me a reference or the relevant part of the > manual from where I could find out how to solve this problem. > > Thanking you in advance for your help, > > > Miguel > - -- > Miguel Ortiz Lombard=EDa > Centro de Investigaciones Oncol=F3gicas > C/ Melchor Fern=E1ndez Almagro, 3 > 28029 Madrid, Spain > Tel. +34 912 246 900 > Fax. +34 912 246 976 > email: mol...@ya... > www: http://www.pangea.org/mol/spip.php?rubrique2 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Le travail est ce que l'homme a trouv=E9 de mieux > pour ne rien faire de sa vie. (Raoul Vaneigem) > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.6 (GNU/Linux) > > iD8DBQFGNc3JF6oOrDvhbQIRAuc0AJ9f3sbpT5pxRvGCPF+T3nSfRNa6WQCeN5pW > 4xyC1vp6uezlnfa6kS0dzmU=3D > =3D6pvr > -----END PGP SIGNATURE----- > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > |
From: Miguel O. L. <mol...@ya...> - 2007-04-30 13:32:02
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Todd, Thank you very much, that's all I needed to know. I was unsure where the hydrogens were taken from. Do you know of any tool that would translate a pdb (including the CONECT records) into the xml format as defined in AA.xml? If not, I will try to write one, but won't be immediate :-) Thanks again! Miguel Todd Dolinsky escribió: > Hi Miguel - > > Modifying the DAT file, as you can probably tell, will only let > PDB2PQR know how to assign charges to already existing atoms, not > rebuild missing hydrogens. You may want to play around with adding > the custom LYR residue (using LYS as a model) to the AA.xml file - > this has a reference coordinate set which will potentially allow you > to rebuild hydrogens accordingly. This is somewhat outside the scope > of what's currently supported (I haven't tested how well it works), > but in theory you should be able to force PDB2PQR to add hydrogens > this way. > > Todd > > > On 4/30/07, Miguel Ortiz Lombardia <mol...@ya...> wrote: > Dear all, > > (Sorry for cross-posting with pdb2pqr, but I didn't get any answer from > there) > > I'm using pdb2pqr version 1.1.2, and have now also tried now with 1.2.1 > > I have added a new residue (a modified lysine) to the CHARMM.DAT > force-field data, in fact making a copy to CHARMM_LYR.DAT. I have also > copied CHARMM.names to CHARMM_LYR.names without further editing. This a > lysine bound to retinal, that I call LYR. I have introduced all the > hydrogens with charges, radii and epsilon (or atom type for the 1.2.1 > version). However, when I run: > > pdb2pqr --ff=CHARMM_LYR file.pdb file.pqr > > the hydrogens are not added to the LYR residue and hence its total > charge is wrong and fractional. > > I must be missing something... I suppose I should be telling how the > hydrogens are added and how this modified amino-acid gets connected to > the rest of the protein, but I couldn't find how to do it. I would > appreciate if you can give me a reference or the relevant part of the > manual from where I could find out how to solve this problem. > > Thanking you in advance for your help, > > > Miguel >> - ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ apbs-users mailing list apb...@li... https://lists.sourceforge.net/lists/listinfo/apbs-users >> - -- Miguel Ortiz Lombardía Centro de Investigaciones Oncológicas C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain Tel. +34 912 246 900 Fax. +34 912 246 976 email: mol...@ya... www: http://www.pangea.org/mol/spip.php?rubrique2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Le travail est ce que l'homme a trouvé de mieux pour ne rien faire de sa vie. (Raoul Vaneigem) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) iD8DBQFGNe/gF6oOrDvhbQIRAsm0AJ49FMGM1HBkiihsEX7wqP/n8C5GcgCbBMBi M3Eukudo2ejkAD9KNAZNcpA= =1zot -----END PGP SIGNATURE----- |