From: Jose Ramon Blas <>
Date: Thu 30 Nov 00 20:38:32 -0800

I hope you will be helpful for me.
I want to simulate a box with acetonitrile as solvent. The strategy that I have followed so as to mantain its straight nature has been to create a triangular molecule, joining both ends by an extra bond by using PREP. This structure has been loaded in
xleap to build topology & coordinates.

        1)minor problem. XLEAP complains about the sp0 nature of the main atoms(this has been solved by adding some dummy atoms by PREP and reloading). This is a detail.

        2)Major problem. When running a SHAKE MD of this system, the Temperature increases and the simulations fails due to a SHAKE error. I have tried to perform SHAKE only on the H-atoms (ntc=2) with the same result. Even removing SHAKE (nstep=0.0005) I find
an increase in T.

        QUESTION: Is there any way of building an acetonitrile with only 3 atoms with Xleap and then impose distance constraints fully respected during the MD simulation?

        Tank you very very much in advance,


P.D. I'm using AMBER5 and the parameters are OK.

J.R. Blas
Dept.Bioquimica i Biol.Molecular   phone: + 34 93 403 58 58
Facultat de Quimica                FAX:   + 34 93 402 12 19
Universitat de Barcelona         
Marti i Franques,1                
08028 Barcelona
Received on Thu Nov 30 2000 - 20:38:32 PST
Custom Search