[gmx-users] Problem in making index.ndx and disres.itp

[Justin Lemkul]

On 3/16/15 9:17 AM, Tushar Ranjan Moharana wrote:
> Hi Justine,
> As you can see in my .itp file the atom number starts from 1. Even this is
> the case with index file. I tried to modify index file to have atomic
> number same as pdb file but it gave a blank output. So my first concern is
> how GROMACS will know which atom I want to restrain? shall I change the
> atom number in itp file to corresponding atom number in pdb?

Topology numbering is based on the [moleculetype], not the global numbers in the 
coordinate file.  You shouldn't adjust anything.

-Justin

> My second concern is the second line of my .itp file looks different from
> the one given in GROMACS website
> As per GROMACS website:
>
> ; ai aj type index type’ low up1 up2 fac
>
>    in my generated itp:
>
> ; i  j ? label      funct         lo        up1        up2     weight
>
> So what do you suggest me to do?
>
> Thanks in advance.
>

-- 
==================================================

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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