[gmx-users] About pdb2gmx

[Justin Lemkul]

On 7/29/12 9:39 AM, vidhya sankar wrote:
> Dear Justin Thank you for your previous reply
>
> When i run the .pdb2gmx_d -f 1OG2O.pdb -o 1OG2O.gro  -p 1OG2O.top   -renum
> It runs successfully. But i have on issue. My PDB contains  HIS residues in both chain A and B I have selected
>
> GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> The .rtp file of this force field does not contain  any [ HIS ] residue
>
> so it takes HIS as HISE  as shown in the cmd prompt
> will ti leads to any poor construction of topology and .gro files ? . How to solve this error?
>

Unless you see the word "error" in the output, then there is no error. 
Histidine protonation states are very sensitive to local environment.  Gromacs 
guesses histidine protonation based on a hydrogen bonding network search, but 
when dealing with metal ions (for example) the outcome can be quite wrong.

-Justin

> Analysing hydrogen-bonding network for automated assigment of histidine
>   protonation. 682 donors and 670 acceptors were found.
> There are 849 hydrogen bonds
> Will use HISE for residue 78
> Will use HISE for residue 184
> Will use HISE for residue 230
> Will use HISE for residue 251
> Will use HISE for residue 276
> Will use HISE for residue 316
> Will use HISE for residue 344
> Will use HISE for residue 353
> Will use HISD for residue 368
> Will use HISE for residue 396
> Will use HISE for residue 410
> Will use HISE for residue 411
> Will use HISE for residue 411
> Identified residue PRO30 as a starting terminus.
> Identified residue HIS411 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
>
>
>
> Processing chain 2 'B' (3702 atoms, 462 residues)
> Analysing hydrogen-bonding network for automated assigment of histidine
>   protonation. 682 donors and 670 acceptors were found.
> There are 830 hydrogen bonds
> Will use HISE for residue 78
> Will use HISE for residue 184
> Will use HISE for residue 230
> Will use HISE for residue 251
> Will use HISE for residue 276
> Will use HISE for residue 316
> Will use HISE for residue 344
> Will use HISE for residue 353
> Will use HISD for residue 368
> Will use HISE for residue 396
> Will use HISE for residue 410
> Will use HISE for residue 411
> Will use HISE for residue 411
> Identified residue PRO30 as a starting terminus.
> Identified residue HIS411 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
>
>
> Thanks in Advance
> With Regards
>
> S.Vidhyasankar
>

-- 
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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

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