[gmx-users] Solvation Free energy using Amber

Justin A. Lemkul jalemkul at vt.edu
Sat Nov 14 23:32:10 CET 2009

jorge_quintero at ciencias.uis.edu.co wrote:
> Ok Justin, I send You a copy of muy simulation for SFE with two proteins +
> water.  Look the top file structure.  Thanks again.

A quick look at the topologies indicates to me that something is badly broken. 
The net charge on each of your protein subunits is 2.505 in state A, which is 
obviously wrong.  In addition, each subunit .itp file defines the molecule as 
Protein_A, which is also wrong, if you should have Protein_A and Protein_B.

Besides that, I don't feel the desire to do your work for you in terms of 
troubleshooting.  If you want advice on the errors you're seeing, post the error 
messages, as I said before.  Everyone on this list has his/her own work to be 
doing, and we're not asking to do yours as well.  If you want free help, make it 
easy for the people from whom you're asking it. :)



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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