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

[Alan]

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?

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

-- 
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<<