Samik Bhattacharya wrote:
hi, i am simulating a membrane protein inside dppc bilayer and in this
regard i am following justin's tutorial. but i ma facing a problem in
running grompp...whenever i run it is giving error
Program grompp, VERSION 4.0.5
Source code file: grompp.c, line: 362
Fatal error:
number of coordinates in coordinate file (1A68_genbox.gro, 49128)
does not match topology (1A68.top, 48628)
now how to solve this problem? i have first generated the lipid box
with the protein then solvated it. i really need little bit of help to
proceed to the next step...
The answer to this question is always the same. You did not correctly update
your topology after some preparation step. You are off by 500 atoms, which, if
you are using DPPC like the tutorial, corresponds to 10 lipids. Look at what
you've done carefully.
-Justin
Thaking You...
Shamik
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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