I know that no missing atom is here. As the fatal error is about atom name CA, I checked it, but it's actually existed in both .rtp and pdb in agreement. Please help me, I don't know what to do :(
Sincerely, Shima ----- Original Message ----- From: Justin A. Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Wednesday, June 27, 2012 8:58 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 12:25 PM, Shima Arasteh wrote: > You mean the order of C and O should be changed in .pdb file? If yes, it > didn't work! > The order of atoms in the .pdb file is irrelevant. What may be the issue is that when pdb2gmx is reporting the error, it is printing its own internal residue number (i.e., the second residue in the chain) - are you missing residue 1? Files downloaded from the PDB are also convenient because they report all missing atoms with "MISSING" entries in the header of the file. These entries will indicate problems before even running pdb2gmx. -Justin > > Sincerely, > Shima > > > ----- Original Message ----- > From: shounakb <bane...@rpi.edu> > To: gmx-users@gromacs.org > Cc: > Sent: Wednesday, June 27, 2012 8:39 PM > Subject: [gmx-users] Re: pdb2gmx error > > Hi, > C and O should go last (i.e. their atom numbers should be 14 and 15 > respectively. > Hope this works! > > Regards, > Shounak > > Shima Arasteh wrote >> >> Hi all, >> >> I got this error : >> Atom CA is used in an interaction of type improper in the topology >> database, but an atom of that name was not found in residue number 2. >> I checked the pdb file and rtp file. >> .rtp file: >> [ SER ] >> [ atoms ] >> N N -0.280 0 >> H H 0.280 0 >> CA CH1 0.000 1 >> CB CH2 0.150 2 >> OG OA -0.548 2 >> HG HO 0.398 2 >> C C 0.380 3 >> O O -0.380 3 >> >> .pdb file: >> >> ATOM 10 N SER 2 -3.181 3.235 3.442 >> ATOM 11 CA SER 2 -3.363 4.671 3.524 >> ATOM 12 C SER 2 -4.135 5.054 4.778 >> ATOM 13 O SER 2 -5.272 4.628 4.966 >> ATOM 14 CB SER 2 -4.138 5.196 2.320 >> ATOM 15 OG SER 2 -4.296 6.612 2.437 >> >> I guess they are in agreement, so what's the problem? >> >> >> >> >> Sincerely, >> Shima >> -- >> gmx-users mailing list gmx-users@ >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Only plain text messages are allowed! >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-request@. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/pdb2gmx-error-tp4998845p4998848.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
