Fwd: [gmx-users] Invalid atom number 6415 in indexfile

[Liu Shiyong]

Thanks.

 Summary:

 1) *.gro from pdb2gmx has no chain id information
 2)  pdb2gmx has an option to output pdb file
 3) If you want to make groups based on chain id :

   pdb2gmx  -ignh -ff ${forcefield} -f input.pdb -o a.pdb
   make_ndx -f a.pdb  -o a.ndx > a.output.make_ndx

  4)  mdrun has an option to output the minimized structure.

 Thanks to all.




On Thu, Jan 29, 2009 at 12:26 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Liu Shiyong wrote:
>
>
>> *.gro has no chain id information.
>> I can not make energy group(based on chain id) from *.gro file generated
>> by pdb2gmx
>>
>
> See the mail I just sent.
>
>
>
>>
>>
>>    3. Don't strip H, just to add them back again :)
>>
>>
>> I have the structure minimized.pdb after EM.
>>
>> minimized.pdb is output from mdrun with -c option.
>>
>> I tried to feed this structure into pdb2gmx.
>> I got an error.
>>
>> Processing chain 1 'A' (5360 atoms, 535 residues)
>> There are 803 donors and 760 acceptors
>> There are 1025 hydrogen bonds
>> Will use HISB for residue 212
>> Will use HISB for residue 223
>> Will use HISB for residue 277
>> Will use HISB for residue 280
>> Will use HISB for residue 374
>> Will use HISB for residue 380
>> Will use HISB for residue 386
>> Will use HISB for residue 398
>> Will use HISB for residue 425
>> Will use HISB for residue 440
>>
>> -------------------------------------------------------
>> Program pdb2gmx, VERSION 3.3.3
>> Source code file: ../../../../src/kernel/pdb2gmx.c, line: 421
>>
>> Fatal error:
>> Atom HD1 in residue HISB 212 not found in rtp entry with 14 atoms
>>             while sorting atoms. Maybe different protonation state.
>>             Remove this hydrogen or choose a different protonation state.
>>             Option -ignh will ignore all hydrogens in the input.
>> -------------------------------------------------------
>>
>>
> Without -ignh, pdb2gmx expects all atoms to present and appropriately
> named. This is one of the more useful error messages, since it tells you
> exactly how to fix the problem.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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-- 
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab:    http://vakser.bioinformatics.ku.edu/people
Phone:      (785) 864-1962
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