[gmx-users] Re: -ighn failing with ffamber

[Justin A. Lemkul]

Alan wrote:
> Thank you Justin,
> 
> You noticed well that. But this example was built to work without
> -ignh and to exemplify my problem, because in real case I have this
> protein and either I can use 'sed' to fix it (mainly H names) I found
> it annoying sometimes, so why not -ignh?
> 

No idea.  I can successfully process your .pdb file with and without -ignh, and 
I get the same result (a correct topology) each time.  Have you run the test 
suite to validate your installation?  Maybe if you post the details of your 
hardware, compilers, OS, etc. someone can spot something that might be 
problematic (i.e., a bug).

-Justin

> Cheers,
> Alan
> 
> On Mon, Jun 15, 2009 at 15:51, <gmx-users-request at gromacs.org> wrote:
> 
>> 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
> 

-- 
========================================

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

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