Do you have the right number of atoms indicated on the second line of the .gro
file? What is in your [molecules] directive in your topology?
-Justin
Marysa van den Berg wrote:
Hi,
I have a problem with Gromacs. I want to do MD simulations with my
proteïn in a DPPC-membrane.
Therefore I followed Justin Lemkul's tutorial on membrane proteïn
simulation. I just used a bigger
membrane (256 lipids instead of 128). I managed to correctly embed the
proteïn in the bilayer,
I solvated it with genbox and then I want to add ions. But when I use
grompp to get a .tpr
file for genion, Gromacs fives the following error:
/Program grompp, VERSION 4.0.7
Source code file: ../../gromacs-4.0.7/src/kernel/grompp.c, line: 320/
/Fatal error:
No molecules were defined in the system
/
I did update my topology in the [ molecules ] section and checked it
twice to see if it fits with
the .gro file. It is correct, so I don't know what the problem is.
Before the solvation there was
no problem with grompp, so it must have something to do with the
solvation? I hope someone
can help me.
Thanks,
Marysa van den Berg
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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