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...
found:
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.
found:
0 atoms
0 bonds
0 angles
0 torsions
Error: pdb and rdparm disagree on number of atoms!
What do i need to do???
Thanks
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 25 2018 - 08:30:03 PST
