Hi, C and O should be atoms 14 and 15 (i.e. the last two atoms) Hope this works! 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 >
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