On 7/31/13 10:07 AM, chinnu657 wrote:
Thanks Justin. So, I've understood how to calculate the number of
coordinates. That in the topology file matches the amount I calculated (as
per how you just taught me).
I want to put 2 proteins in the same box. I did this by changing the
topology files of the respective proteins to itp. Then a new top file was
made in which the itp files were included. I pasted the contents earlier.
After this, performed editconf separately on each .gro file and combined
them together. then I solvated them. Right before neutralising using genion,
while using grompp to get the tpr file is where the error about the mismatch
happens.
How can I solve this? I've tried making sure my topology file is updated at
every stage.
The most common source of problem is water molecules not being accurately
accounted for, but the difference cited in the error message is 20, so it's
probably not the waters. I can't tell based on the description exactly what you
did. As I said before, an exact sequence of commands (copied and pasted from
the terminal) is helpful. Concatenating coordinate files is precarious, as you
have to conduct manual deletions of lines to "fix" them after combining them.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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