[gmx-users] how to name HIS in the input pdb for the pdb2gmx

[Brett]

Dear All，
 
If we change HIS188 in Chain B to HISE188 in Chain B, before change the PDB looks like
"HIS B  188", but after change the PDB will look like "HISEB 188", which makes thereis no space between "HISE" and "Bchain". I do not know whether pdb2gmx can recognize HISEB 188, or we process it in some other way.
 
I am looking forward to getting a reply from you.
 
Brett








At 2015-04-26 11:08:19, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 4/25/15 11:05 PM, Brett wrote:
>> Dear All,
>>
>> For gromacs, for HIS residues there are HISD,HISE and HISH. In the original PDB file, are HIS residues are written as HIS. If based on necessity, I change exactly some HIS to HISD, some HIS to HISE and some HIS to HISH,the coordinate lines contaning HISD,HISE and HISH will not aling with all the other coordinate lines. Does pdb2gmx recognize these non-aligned coordinate lines? Or what other strategy you recommend me to take so that pdb2gmx can recognize HISD,HISE and HISH?
>>
>
>Do the replacement properly and don't screw up column alignment.  It needs to be 
>correct for proper interpretation of the coordinates.
>
>-Justin
>
>-- 
>==================================================
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>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
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