[AMBER] amb2gmx

From: roja rahmani <roja.rhmn.gmail.com>
Date: Sat, 3 Feb 2018 10:45:46 +0330

Hi,i'm beginner. i use AMBERtools17, and i want to convert .prmtop and
.incprd files to GROMACS topology files.i use this script
https://github.com/choderalab/mmtools/blob/master/converters/amb2gmx.pl

>> perl amb2gmx.pl --prmtop sustiva.prmtop --crd sustiva.inpcrd --outname
sustiva
 and i get this error;

sh: ambpdb: command not found
sh: rdparm: command not found
Parsing PDB file sustiva.pdb...
found:
    0 protein or solute residues
    0 sodium ions
    0 chloride ions
    0 magnesium ions
    0 waters

    0 TOTAL residues read
Reading coordinates from CRD file...Reading prmtop file...
0 atom type indices read.

found:
        0 atoms
        0 bonds
        0 angles
        0 torsions
BAD BOX OR BOX NOT DETECTED; USING DUMMY BOX SIZE IN GRO FILEBAD BOX OR BOX
NOT DETECTED; USING DUMMY BOX SIZE IN GRO FILE
Qtot = 0
Qmax = 0 at atom -1

Constructing list of unique nonbonded atomtypes...
0 unique atomtypes found.
Writing atom types...
Done.
would you please help me?

Thank you
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 02 2018 - 23:30:02 PST
Custom Search