hi On Thursday 06 April 2006 01:28, vincenzo venditti wrote: > Dear all, > I runned a MD simulation on an RNA molecule containing a modified residue > using amber. I inserted the same parameters for the modified residue in > both amber and gromacs (amber ff port) force field. At the end of the > simulation I renamed the trajectory file specifing the g87 extension. Then > I prepared a tpr file for gromacs, starting from the same pdb file that I > used to generate the amber input files. Gromacs read both the pdb and the > trajectory files without any error or warning. But now I have two problems: > 1) the distances that should be in Angostrom units are now in nm units. > 2)I roughly overcome the first problem compiling a macro for MOLMOL that > automatically add the bonds, but I saw that the modified residue atoms > (only that) give a very distorted structure while in the original > trajectory they showed a very nice behaviour. Have you any suggestions? > Thanks in advance, > Vincenzo
for 1) there is a workaround i think first posted on http://mccammon.ucsd.edu/ied/ use following patch: --- trxio.c 2002-02-28 02:49:31.000000000 -0800 +++ trxio.c 2003-12-12 17:11:34.000000000 -0800 @@ -453,14 +453,14 @@ /* else eof! */ return FALSE; } - x[i][m]=x0; + x[i][m]=x0 * 0.1; } } if (bReadBox) { for(m=0; (m<DIM); m++) { if (fscanf(status,"%lf",&x0) != 1) return FALSE; - box[m][m]=x0; + box[m][m]=x0 * 0.1; } } return TRUE; beware that you will always get than smaller values by factor 10. for 2) can only guess ... > > Videochiamata? Prova MSN Messenger: divertente, facile, veloce, gratuito! -- Florian ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Mailto: florian.haberl AT chemie.uni-erlangen.de -------------------------------------------------------------------------------
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