[gmx-users] -ighn failing with ffamber

[Justin A. Lemkul]

Alan wrote:
> 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)
> 

I don't know why this is failing, but from the looks of your .pdb file, you have 
all the atoms you need, properly named and everything.  Why do you need -ignh?

-Justin

> -------------------------------------------------------
> 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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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================