[gmx-users] About pdb2gmx

[tarak karmakar]

see its not a big issue. Look at the atom types of the particular
RESIDUE in the pdb file and also have a look into the atom types
present in the rtp file. Now if these are matching properly then you
can choose any convenient name for that particular residue in the rtp
file. But the name of the particular residue should be exactly same in
the two files.

On Sun, Jul 29, 2012 at 7:09 PM, vidhya sankar <scvsankar_agr at yahoo.com> 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?
>
> 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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-- 
Tarak