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

[Mark Abraham]

Hi,

Files in fixed-column formats use the column widths to separate elements.
They don't use white space at the same time, for the same job! Try it and
see ;-)

Mark
On 26/04/2015 6:29 am, "Brett" <brettliu123 at 163.com> wrote:

> 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
> >
> >--
> >==================================================
> >
> >Justin A. Lemkul, Ph.D.
> >Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> >Department of Pharmaceutical Sciences
> >School of Pharmacy
> >Health Sciences Facility II, Room 629
> >University of Maryland, Baltimore
> >20 Penn St.
> >Baltimore, MD 21201
> >
> >jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >http://mackerell.umaryland.edu/~jalemkul
> >
> >==================================================
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