On 2/27/13 11:14 AM, swati rana wrote:
Thanx a lot that helped... but now there is one more issue. I am consulting
the site for each and every error and getting most of the help but these
are few which i am not able to resolve even after referring to the site.
After running the energy minimization step i am facing the following error:
-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/confio.c, line: 801
Fatal error:
Something is wrong in the coordinate formatting of file system.gro. Note
that gro is fixed format (see the manual)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I am not able to understand that in system.gro file do we have to do the
change in the no of atoms according to the inflated_system.gro file or not.
No, the number of atoms in the coordinate file should be correct. InflateGRO
does this for you.
Another thing is if i am adding Chloride ions to equalize the charge do i
have to reduce the no of POPC molecules or not. Kindly suggest what should
During inflation and shrinking, you should not be adding solvent or ions. You
will get a nonsensical result.
be done i looked into the system.gro file and also the line it is referring
to i did not find anything unusual. But there is a catch its the same
molecule LEU which was having link to NH3.
Probably a visualization artifact. Real bonds are set in the topology, not in
whatever the visualization program guesses.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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