On 2/27/13 10:03 AM, swati rana wrote:
Hi all,
After running the following command
<b>perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5
area.dat</b>
I modified the lipids in the topol.top file and in system.gro file the no
of lipids and no of atoms respectively.
but after that for energy minimization when i ran the following command:
<b>grompp -f EM.mdp -c system.gro -p topol.top -o em.tpr</b>
It is showing the following error. Please tell me if the command is right
or not and if it is right then what can be done to resolve and why exactly
it is showing this error. I checked the topology file but i am not able to
reach any conclusion. Please guide me as most of you have faced this error
and got the solution for it .
<b>Ignoring obsolete mdp entry 'title'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
Generated 867 of the 1891 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 3 bonded neighbours molecule type 'POPC'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file topol.top, line 21239]:
System has non-zero total charge: 3.000002
Total charge should normally be an integer. See
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line: 523
Fatal error:
number of coordinates in coordinate file (system.gro, 10019)
does not match topology (topol.top, 17093)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors</b>
Did you consult the website? The answer is always the same...
If the numbers don't match, then your bookkeeping was incorrect. Your topology
specifies more atoms than your coordinate file, so you did not correctly account
for the deletion of lipids or water. Note that above, grompp is looking for
SOL, but InflateGRO deletes all solvent from the input file, so you need to
remove them from your topology as well.
-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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