Hi there, I am trying to understand why when doing: pdb2gmx -f GGG.pdb -ff amber99sb -ignh
I am getting: WARNING: atom H is missing in residue GLY 2 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) ------------------------------------------------------- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.c, line: 704 Fatal error: There were 1 missing atoms in molecule Protein_G, if you want to use this incomplete topology anyhow, use the option -missing ------------------------------------------------------- in /sw/share/gromacs/top/ffamber99sb.hdb I have: GLY 2 1 1 H N -C CA 2 6 HA CA N C And I see nothing wrong with that. in /sw/share/gromacs/top/ffamber99sb.rtp: [ GLY ] [ atoms ] N amber99_34 -0.41570 1 H amber99_17 0.27190 2 CA amber99_11 -0.02520 3 HA1 amber99_19 0.06980 4 HA2 amber99_19 0.06980 5 C amber99_2 0.59730 6 O amber99_41 -0.56790 7 Which is pretty OK too. Besides, I don't get any error for NGLY or CGLY. Only "atom H is missing in residue GLY 2". If I mess with ffamber99sb.hdb for GLY I got others messages stating the other missing atoms. OPLS, which is very similar, works fine. The pdb is as simple as this: ATOM 1 N NGLYG 1 59.012 0.129 -0.254 1.00 0.00 ATOM 2 H1 NGLYG 1 58.484 0.488 0.618 1.00 0.00 ATOM 3 H2 NGLYG 1 58.683 0.775 -1.007 1.00 0.00 ATOM 4 H3 NGLYG 1 58.789 -0.895 -0.326 1.00 0.00 ATOM 5 CA NGLYG 1 60.467 0.239 -0.366 1.00 0.00 ATOM 6 HA1 NGLYG 1 60.728 1.248 -0.251 1.00 0.00 ATOM 7 HA2 NGLYG 1 60.773 -0.150 -1.355 1.00 0.00 ATOM 8 C NGLYG 1 61.175 -0.584 0.690 1.00 0.00 ATOM 9 O NGLYG 1 60.636 -0.753 1.809 1.00 0.00 ATOM 10 N GLY G 2 62.471 -1.163 0.322 1.00 0.00 ATOM 11 H GLY G 2 62.882 -1.173 -0.678 1.00 0.00 ATOM 12 CA GLY G 2 63.150 -1.717 1.498 1.00 0.00 ATOM 13 HA1 GLY G 2 62.745 -2.672 1.656 1.00 0.00 ATOM 14 HA2 GLY G 2 63.047 -1.068 2.389 1.00 0.00 ATOM 15 C GLY G 2 64.648 -1.799 1.285 1.00 0.00 ATOM 16 O GLY G 2 65.151 -2.016 0.165 1.00 0.00 ATOM 17 N CGLYG 3 65.503 -1.595 2.460 1.00 0.00 ATOM 18 H CGLYG 3 65.152 -1.325 3.447 1.00 0.00 ATOM 19 CA CGLYG 3 66.902 -1.817 2.091 1.00 0.00 ATOM 20 HA1 CGLYG 3 67.178 -1.043 1.438 1.00 0.00 ATOM 21 HA2 CGLYG 3 67.022 -2.819 1.632 1.00 0.00 ATOM 22 C CGLYG 3 67.808 -1.809 3.299 1.00 0.00 ATOM 23 OC1 CGLYG 3 67.222 -1.605 4.509 1.00 0.00 ATOM 24 OC2 CGLYG 3 69.135 -2.006 3.077 1.00 0.00 My memory may fail, but I can swear it was working before... Many thanks in advance, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<<
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