[gmx-users] Problem importing PDB to Gromacs

[tarak karmakar]

Remove all the hydrogens from the pdb file and then try to run pdb2gmx, I
hope it'll do fine.
Or you can also use -ignh option as suggested by Justin.

Tarak


On Fri, May 10, 2013 at 3:35 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/10/13 5:16 AM, Jernej Zidar wrote:
>
>> Hi,
>>    In CHARMM I generated a short peptide. The N-terminal is a regular
>> -NH2 (patch NNEU) while  the C-terminal is amidated (patch CT2).
>>
>>    I would like to import the PDB to GROMACS using pdb2gmx by using the
>> CHARMM27 forcefield later. I issue the following command:
>>   pdb2gmx -v -f irik-l.pdb -inter
>>
>> and choose the appropriate protonation states of the aminoacids, the
>> N-/C- terminal patches, solvent but the import fails:
>> Program pdb2gmx, VERSION 4.6
>> Source code file: /home/zidar/utils/gromacs-4.6/**src/kernel/pdb2gmx.c,
>> line: 727
>>
>> Fatal error:
>> Atom H1 in residue ILE 1 was not found in rtp entry ILE with 20 atoms
>> while sorting atoms.
>>
>> For a hydrogen, this can be a different protonation state, or it
>> might have had a different number in the PDB file and was rebuilt
>> (it might for instance have been H3, and we only expected H1 & H2).
>> Note that hydrogens might have been added to the entry for the N-terminus.
>> Remove this hydrogen or choose a different protonation state to solve it.
>> Option -ignh will ignore all hydrogens in the input.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors>
>> - - - -
>>
>>    Atom H1 (and H2) is the atom from the both the N-/C- terminals that
>> in CHARMM is part of the residue ILE but Gromacs (4.6.1) does not
>> recognize it properly as they are renamed:
>> Renaming atom 'HT1' in residue 1 ILE to 'H1'
>> Renaming atom 'HT2' in residue 1 ILE to 'H2'
>>
>>    How can one solve this problem?
>>
>>
> Have you tried -ignh like the error output suggests?
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>