Artur Panczakiewicz wrote:
Dear Gromacs Users,
I'm a freshman and would like to lear how to use GROMACS in my
research starting from tutorial. I've just installed the newest
version and try to repeat all of the steps from the chapter that
describes the preparation of Ribonuclease A to MD simulation. In my
case it is not possible, unfortunatelly. The grompp program crashes
such a way:
-------------------------------------------------------
Program grompp, VERSION 4.5.1
Source code file: toppush.c, line: 1987
Fatal error:
No such moleculetype SOL
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I tried to install GROMACS on other machine with different Linux
distribution but the error in grompp was the same.
What is important, I installed version 4.0.7 and it works well! I
don't have any idea what is going on.
Does anyone have a similar problem?
Did you follow the link provided by grompp? There is some helpful information
there...
http://www.gromacs.org/Documentation/Errors#Fatal_error.3a_No_such_moleculetype_XXX
Was there water in the input structure? There have been some changes to pdb2gmx
since the 4.0.x series, perhaps related to the way water is named/renamed.
Check what is in your coordinate file (before pdb2gmx and after), what is in
your topology, and whether any of this is wrong or unexpected.
-Justin
Regards,
Artur
--
========================================
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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