[gmx-users] Issue with GROMACS file format

Justin Lemkul jalemkul at vt.edu
Mon Jul 23 18:40:16 CEST 2012

On 7/23/12 12:32 PM, SatyaK wrote:
> Hello All,
> I have an issue with converting a .dat file into GRO format and viewing it
> in VMD. Say, we have {x, y,z} ={0,0,10000} in A.
>    ----> Converted GRO file (in nm):  171OHX     OW 5000  0  01000.000
> The Z coordinate has 8 places which is apt as per the Gro format.
> However,when VMD reads this coordinate, it is assuming Z coordinate as
> 000.00 instead of 1000.000. Can someone help me find out the issue.

Hard to tell from the email, but it appears that your format is wrong for the 
other columns.  A .gro file has a fixed format that requires certain alignment 
of all the information:




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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