[gmx-users] can gromacs read amber trajectory

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Mon Feb 20 10:08:29 CET 2006


On Sunday 19 February 2006 00:16, Lydia wrote:
>    Now I know why it didn't work: I need to use -b to give an initial time.
> (Sorry that I didn't know that before. I've just started to use gromacs.) 
> I appreciate your help greatly.
> sincerely
> lydia

take a look at: http://mccammon.ucsd.edu/ied/


Notes for using GROMACS to analyze AMBER trajectories

These notes are of mostly historical interest, now that IED is able to read 
output from Ptraj. In general it will be easier to analyze AMBER trajectories 
with Ptraj than with GROMACS.

GROMACS can be used to analyze trajectories produced by the SANDER module of 
AMBER. GROMACS will read the AMBER trajectory if it is renamed to have an 
extension of .g87 . GROMACS will not read the AMBER prmtop topology file, but 
you can produce a pdb file to use as the topology file like this

ambpdb -p prmtop <prmcrd >topol.pdb

There is one problem with using GROMACS to analyze AMBER data: GROMACS assumes 
coordinates are in nanometers, while AMBER writes them in Angstroms.You can 
ignore this problem, in which case all your atoms will be ten times further 
apart than they should be in IED. Since VMD uses distances to determine 
bonding for PDB files, this means that if you use a PDB topology file, you 
won't see any bonds. If you use the van der Waals representation (with an 
increased radius) and remember to divide any distances you measure by 10, 
this may be acceptable.

If you are comfortable with recompiling GROMACS, you can use the following 
patch so that your distances will be correct and bonds will appear. Note that 
with this patch, all .g87 files are assumed to be in units of Angstroms, so 
if you think you may actually need to read a .g87 file in units of 
nanometers, this may not be a good idea.

The following patch should be applied to src/gmxlib/trxio.c

--- 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;


i think there could be than a problem with different naming of amber aa.

something like: 

sed -e "/ATOM/s/HIP/HIS/g" 
sed -e "/ATOM/s/HID/HIS/g"
sed -e "/ATOM/s/HIE/HIS/g" 
sed -e "/ATOM/s/CYX/CYS/g"

should change pdb naming.

Also the "bruteforce" thing is possible: Transfer it to a multiple pdb file 
and read it back in gromacs ...



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

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