[gmx-users] AMBER-GROMACS conversion

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Thu Apr 6 09:16:02 CEST 2006


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 

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 ...

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 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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