Sorry if I made someone more confuse, I thought this was the problem. Probably reading the original post again would have a wise step.
Itamar On Wed, Nov 11, 2009 at 7:25 PM, Tsjerk Wassenaar <[email protected]> wrote: > Hi, > > Well, -ignh is not the right answer here. I recall that just a few > days ago someone posted the same problem. For Amber you need to tag > the first and last residue. For your GLY, it means you have to rename > it to NGLY. > > Itamar, > > The warning mentions an atom missing from the .pdb file. These have to > be built according to the rules in the .hdb file. The option -ignh is > to strip off hydrogen atoms that are present in the .pdb file, but are > not listed in the .rtp file and are thus not part of the residue > according to the force field. Please make sure that your replies are > to the point, because replies that are amiss may confuse the original > poster and bring them even further from solving their problems. > > Cheers, > > Tsjerk > > On Wed, Nov 11, 2009 at 9:16 AM, Itamar Kass <[email protected]> wrote: >> Hi, >> >> Try to use -ignh. >> >> On Wed, Nov 11, 2009 at 7:09 PM, leila karami <[email protected]> >> wrote: >>> I do command pdb2gmx but follow warning and error is came up: >>> >>> WARNING: atom H is missing in residue GLY 1 in the pdb file >>> You might need to add atom H to the hydrogen database of residue >>> GLY >>> in the file ff???.hdb (see the manual) >>> >>> Fatal error: >>> There were 1 missing atoms in molecule Protein_A, if you want to use this >>> incomplete topology anyhow, use the option -missing >>> >>> my pdb file is: >>> >>> HETATM 1 N GLY A 1 19.949 29.046 10.462 >>> HETATM 2 CA GLY A 1 19.485 28.078 9.486 >>> HETATM 3 C GLY A 1 20.152 28.247 8.136 >>> HETATM 4 O GLY A 1 19.859 29.193 7.405 >>> HETATM 5 1H GLY A 1 20.545 29.773 10.181 >>> HETATM 6 2HA GLY A 1 19.690 27.084 9.856 >>> HETATM 7 2H GLY A 1 20.356 28.562 11.250 >>> HETATM 8 3H GLY A 1 19.099 29.546 10.681 >>> HETATM 9 1HA GLY A 1 18.415 28.236 9.347 >>> >>> and my ffamber03.hdb of gly is >>> >>> GLY 2 >>> 1 1 H N -C CA >>> 2 6 HA CA N C >>> >>> NGLY 2 >>> 3 4 H N CA C >>> 2 6 HA CA N C >>> >>> how I add H to hdb file? >>> >>> -- >>> gmx-users mailing list [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > Computational Chemist > Medicinal Chemist > Neuropharmacologist > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
