Hi Leila, I think it is a pdb format problem. According to pdb convention, column 17 should be left blank and columns 18-20 are used for residue name.
Please check your pdb format first. Good luck. Terry 2009/11/21 leila karami <karami.lei...@gmail.com> > Hi > > I used amber03 force field in gromacs to study pr-dna interaction. > I compare my pdb file and ffamber03.rtp file. > I should correct my pdb file to tally with rtp file. N-terminal (NUMBER 1) > and C-terminal (NUMBER 70) of my protein is GLY. > pdb file and rtp file relating to gly1 and gly70 are placed in follow. > > pdb file of gly1: > > 1 N NGLY 1 > 2 CA NGLY 1 > 3 C NGLY 1 > 4 O NGLY 1 > 5 1H NGLY 1 > 6 2HA NGLY 1 > 7 2H NGLY 1 > 8 3H NGLY 1 > 9 1HA NGLY 1 > > rtp file of gly1: > > [ NGLY ] > [ atoms ] > N amber99_39 0.29430 1 > H1 amber99_17 0.16420 2 > H2 amber99_17 0.16420 3 > H3 amber99_17 0.16420 4 > CA amber99_11 -0.01000 5 > HA1 amber99_28 0.08950 6 > HA2 amber99_28 0.08950 7 > C amber99_2 0.61630 8 > O amber99_41 -0.57220 9 > > pdb file of gly70: > > 1 N CGLY A 70 > 2 CA CGLY A 70 > 3 C CGLY A 70 > 4 O CGLY A 70 > 5 H CGLY A 70 > 6 2HA CGLY A 70 > 7 1HA CGLY A 70 > 8 OXT CGLY A 70 > 9 CGLY A 70 > > rtp file of gly70: > > [ CGLY ] > [ atoms ] > N amber99_34 -0.38210 1 > H amber99_17 0.26810 2 > CA amber99_11 -0.24930 3 > HA1 amber99_19 0.10560 4 > HA2 amber99_19 0.10560 5 > C amber99_2 0.72310 6 > OC1 amber99_45 -0.78550 7 > OC2 amber99_45 -0.78550 8 > before correction of pdb file, following warning and error was 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 > * > ffamber03.hdb: > * * > NGLY 2 > 3 4 H N CA C > 2 6 HA CA N C > > I didn't use -missing option. > > please guide me. > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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