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

Irem Altan irem.altan at duke.edu
Wed Jan 18 18:47:10 CET 2017


It still asks for a .tpr file, though:

Command line:
  gmx trjconv -f conf_complete.gro -o file.pdb

Will write pdb: Protein data bank file

-------------------------------------------------------
Program gmx trjconv, VERSION 5.1.2
Source code file: /Users/irem/Downloads/gromacs-5.1.2/src/gromacs/fileio/gmxfio.c, line: 476

Can not open file:
topol.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Best,
Irem

> On Jan 18, 2017, at 6:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> 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
> 
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