[gmx-users] -ighn failing with ffamber

[Alan]

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<<