OK. PDB FILE IS AS BELOW: HETATM 1 C FOR 0 -0.721 1.600 1.249 HETATM 2 O FOR 0 -0.839 2.806 1.453 ATOM 3 N VAL 1 -1.227 0.728 2.125 ATOM 4 CA VAL 1 -1.918 1.159 3.323 ATOM 5 C VAL 1 -1.969 2.678 3.410 ATOM 6 O VAL 1 -0.931 3.335 3.447 ATOM 7 CB VAL 1 -1.219 0.644 4.576 ATOM 8 CG1 VAL 1 0.208 1.178 4.618 ATOM 9 CG2 VAL 1 -1.976 1.118 5.812 ATOM 10 N SER 2 -3.181 3.235 3.442 ATOM 11 CA SER 2 -3.363 4.671 3.524 ATOM 12 CB SER 2 -4.138 5.196 2.320 ATOM 13 OG SER 2 -4.296 6.612 2.437 ATOM 14 C SER 2 -4.135 5.054 4.778 ATOM 15 O SER 2 -5.272 4.628 4.966
Sincerely, Shima ----- Original Message ----- From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Wednesday, June 27, 2012 9:14 PM Subject: Re: [gmx-users] Re: pdb2gmx error On 6/27/12 12:43 PM, Shima Arasteh wrote: > 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 :( > Please copy and paste the entirety of the first three residues in your .pdb file so we can see what you're working with. -Justin > > 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 -- 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
