[gmx-users] About pdb2gmx

[Mark Abraham]

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
>>
>