Andrey A. Koverga wrote:
Hi all! I'm just a beginner user of Gromacs, that's why my question
may seem strange to you. But I hope, that somebody can help me in
solving my problem. The point is that I'm trying to perform the analysis
of tetrabutylammonium cation solvatation using OPLS force field. Earlier
i've modelled tetrametylammonium cation with same force field; the
topology *.itp file for TMA was created, using The Dundee PRODRG Server:
itp-file was created for some Gromacs force field, and than modified by
definition of the UA-groups according to OPLS UA-types. This way is
unsuitable for determination of TBA topology, 'couse in this case
"all-atom" determination should be performed. So that's why I'm asking
your advise what should I do. Thanks a lot!
Read how OPLS was parameterized and do something consistent with that.
Anything else is random number generation (and even this might be!)
Mark
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