[gmx-users] Invalid line in coordinate file (grompp tool)

Justin Lemkul jalemkul at vt.edu
Wed Oct 2 15:39:56 CEST 2013

On 10/2/13 8:45 AM, Andrew Bostick wrote:
> Dear Justin
> Thanks for your quick reply.
> What is reason of this issue?
> My gro file contains 11383 lines.
> 11383-3=11380
> This value is equal to second line.

Sorry, misread your initial post.  One of two things is happening:

1. You've used an editor to modify the file such that newline characters are 
screwing up formatting.
2. There are fewer atoms in the file than you think, given that grompp is still 
looking for atoms when it encounters box vectors.  Use grep -c to check.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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