Dears, Playing with amb2gmx.pl, I have in my topol.top file something like:
[snip] C C 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ... c c 0.00000 0.00000 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 [snip] Then, running grompp, I got several warnings, e.g.: WARNING 1 [file "multi_GMX.top", line 38]: Overriding atomtype c ... Is there any special reason why atomtypes are not case sensitive? Fortunately it seems that all lower case atomtypes from gaff.dat (GAFF) mirrors the upper case of, say, parm99.dat (AMBER 99). But this is not good in MHO. Many thanks in advance. Cheers, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<<
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