[gmx-users] Re: -ighn failing with ffamber
Alan
alanwilter at gmail.com
Wed Jun 17 12:04:33 CEST 2009
Hi Justin,
Just to let you know that after reinstalling everything again with
Fink it worked fine. I have no idea I hade such a problem.
Alan
On Mon, Jun 15, 2009 at 23:05, Alan<alanwilter at gmail.com> wrote:
> Hi Justin,
>
> Please, confirm this, you mean that this pdb worked for you with '-ignh'?
>
> Gosh...
>
> So I may not loosing my mind when I said that it was working before.
>
> So, I am running:
> - Mac Osx 10.5.7 intel.
> - Gromacs 4.0.5 (from Fink) with ffamber;
> - Compilers from Fink.
>
> I ran test suite and although I got some fails for complex and
> kernel, nothing for simple or pdb2gmx.? Anyway, I doubt tested suite
> would fail because oplsaa is working fine here if I do 'pdb2gmx -f
> GGG.pdb -ff oplsaa -ignh'
>
> In any case, many thanks for your attention Justin,
>
> Alan
>
> On Mon, Jun 15, 2009 at 20:01, <gmx-users-request at gromacs.org> wrote:
>> 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
>>>
>>
>
> --
> 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<<
>
--
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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