On 12/13/12 1:34 AM, Shine Devaraj wrote:
Dear users,
I have used grompp command for minimising my protein and ligand in membrane
after using inflategro command.
My system has no problem in visualizing in VMD. The protein is in proper
order
But I am getting the error
-------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: confio.c, line: 728
Fatal error:
Invalid line in system_inf.gro for atom 6835:
25.67360 25.77400 6.59650
-------------------------------------------------------
.............
128DPPC C46 6396 24.164 0.531 3.551
128DPPC C47 6397 24.158 0.578 3.406
128DPPC C48 6398 24.266 0.510 3.321
6835 128DPPC C49 6399 24.248 0.548 3.174
128DPPC C50 6400 24.346 0.469 3.086
25.67360 25.77400 6.59650
Kindly make some light on this.
The second line in a .gro file specifies how many atoms there are. You've
specified too many, since grompp is looking for atom 6835, but it finds box
vectors instead.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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