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
