On 10/2/13 8:21 AM, Andrew Bostick wrote:
Dear users,
I have used grompp command for minimising my system (protein and
membrane). I am getting the error:
-------------------------------------------------------
Program grompp, VERSION 4.5.1
Source code file: confio.c, line: 744
Fatal error:
Invalid line in system.gro for atom 11380:
6.98200 7.63300 7.36400
For more information, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
First and end lines of my gro file are as follows:
Giving Russians Opium May Alter Current Situation
11380
1DMPC C1 1 4.752 4.493 5.267
1DMPC C2 2 4.770 4.549 5.409
.
.
.
.
.
1834SOL OW11378 2.802 5.473 1.849
1834SOL HW111379 2.797 5.377 1.844
1834SOL HW211380 2.812 5.501 1.758
6.98200 7.63300 7.36400
------------------------------------------------------
Number in second line (11380) is equal to number of atoms in gro file
(11380)?
It shouldn't be. The second line in the .gro file specifies the number of
atoms, which should always be (number of lines) - 3 (title, second line, box
vectors at the end).
-Justin
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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