[gmx-users] converting .gro trajectory to .pdb

[Justin Lemkul]

On 1/18/17 12:32 PM, Irem Altan wrote:
> Hi,
>
> It gives me an error saying
>
> Fatal error:
> Index[1556] 3148 is larger than the number of atoms in the
> trajectory file (3145). There is a mismatch in the contents
> of your -f, -s and/or -n files.
>
> I’m guessing this is because I had created the original .gro file by just using the protein heavy atoms, but the .tpr file obviously has the indices according to the entire system.
>

You don't need to do anything as complex as what Dawid suggested.  You just need 
to convert the format:

gmx trjconv -f file.gro -o file.pdb

-Justin

> Best,
> Irem
>
> On Jan 18, 2017, at 4:22 PM, Dawid das <addiw7 at googlemail.com<mailto:addiw7 at googlemail.com>> wrote:
>
> Hi,
>
> I guess you can try
> gmx trjconv -f  file.gro -o file.pdb -pbc mol -s file.tpr -center
>
> 2017-01-18 16:14 GMT+01:00 Irem Altan <irem.altan at duke.edu<mailto:irem.altan at duke.edu>>:
>
> Hi,
>
> I have a trajectory saved in .gro format. It has multiple frames/snapshots
> in it. I’m using .gro format because I needed higher precision than
> standard .pdb precision, but now I can’t visualize it with VMD. I would
> like to convert this to .pdb, and I tried editconf to do this. The problem
> is, it only converts the first frame. How can I convert the entire
> trajectory from .gro to .pdb?
>
> Best,
> Irem
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-- 
==================================================

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

==================================================