On 5/11/2011 1:05 AM, kirubakaran palani wrote:
Dear All
Could any one help me to solve this error in gromacs 4.5.5 version. I
am running dynamics on apo protein and the protein shows negative
charge of -6 (after choosing OPLS-AA force filed) and when i was
neutralizing the -6 with +6 and generating the genion.tpr file there
it shows "No such moleculetype NA+" error. But the same protein was
running with out any error message in gromacs 4.0.7 version.
The naming convention has changed. See share/top/oplsa.ff/ions.itp
Mark
The error message was given below.
Kindly rectify the problem
=======================================================================================
[student@localhost gro]$ grompp -f em.mdp -p topol.top -c genion.gro
-o genem.tpr
Ignoring obsolete mdp entry 'cpp'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
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
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 2 bonded neighbours molecule type 'SOL'
-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: toppush.c, line: 1987
Fatal error:
No such moleculetype NA+
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
========================================================================================
Regards
Kirubakaran P
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists