Moeed wrote:
Dear experts,
I have installed newest version of gromacs (4.5) on our cluster. When I
issue the command below to test installation I get an error about atom type
CU+2. I am not using such atom type at all! Could you please help me what
wrong is. Thanks.
My system contains only C and H atoms!. Force field: OPLSAA
grompp -f *.mdp -c *.gro -p *.top -o out >& output.grompp_md
NOTE 1 [file md-NVT-revised.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
-------------------------------------------------------
Program grompp, VERSION 4.5
Source code file: toppush.c, line: 1166
Fatal error:
Atomtype CU2+ not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
This is probably a bug that has already been fixed, but is only available in the
git repository. The fix is to change the capitalization of both CU2+ and ZN2+
in oplsaa.ff/ions.itp. They should be Cu2+ and Zn2+, respectively. Otherwise,
don't #include "ions.itp" in your topology if you don't need it.
-Justin
--
========================================
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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