On 30/07/2012 8:49 AM, Justin Lemkul wrote:
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.
And you can make selections for individual histidines with an option of
pdb2gmx. But Vidhya knew all of this from reading pdb2gmx -h, right?
Mark
-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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