[AMBER] Problem to convert

From: Alberto Bencomo <bencomom1985.gmail.com>
Date: Thu, 25 Jan 2018 09:23:31 -0700

Hi there:
I am using amb2gmx.pl to obtain the format .top and .gro file to start a MD
simulation with GROMACS. When I put this in a terminal:

./amb2gmx.pl --prmtop jz4.prmtop --crd jz4.inpcrd --outname jz4

obtain this:

| New format PARM file being parsed.
| Version = 1.000 Date = 01/25/18 Time = 09:15:26
sh: 1: rdparm: not found
substr outside of string at ./amb2gmx.pl line 196.
substr outside of string at ./amb2gmx.pl line 197.
Parsing PDB file jz4.pdb...
    1 protein or solute residues
    0 sodium ions
    0 chloride ions
    0 magnesium ions
    0 waters

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

0 atoms
0 bonds
0 angles
0 torsions

Error: pdb and rdparm disagree on number of atoms!

What do i need to do???
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Received on Thu Jan 25 2018 - 08:30:03 PST
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