[gmx-users] error in running MD

[vema aparna]

Dear Gromacs Users,

I am a new user of GROMACS. I would like to run  MD run of a protein with ligand and crystal water bound to it. I have also solvated the system again using the explicit water.

Now my system has the following groups as mentioned in top file

Protein
Ligand
SOL (crystal water)
SOL

I checked to keep both the solvent groups identified as SOL in .gro file.

I was able to minimise the system however, when i try to run dynamics with position restraint. I get an error while preprocessing the file in grompp


Fatal error: Atom 2015 in multiple T-Coupling groups (14 and 2).

Incidentally atom 2015 was found to be the last atom of the ligand. I used the index file. I deleted the group 2 and now i see the message

Fatal error: Atom 2015 in multiple T-Coupling groups (13 and 2).

and this continued untill i deleted all the groups in the index file. But now i got another error

ERROR: SOL group not present


Is it feasible to run MD with both crystal water and explicit water.

Can you suggest me how to rectify this problem.


Thanking you,

Sincerely,

Aparna
==================================
Vema Aparna
Prof. G. R. Desiraju's Group,
School of Chemistry
University of Hyderabad
Hyderabad - 500 046
INDIA
==================================

Vema Aparna
Prof. G. R. Desiraju's Group,
School of Chemistry
University of Hyderabad
Hyderabad - 500 046
INDIA
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20050212/e9e585a5/attachment.html>