It is not a stupid question but you ask your question in the wrong forum.
Again, if you construct a THR residue with the correct atom and residue names for the side chain and the NH3+ and COO- termini. You will have no problem to have the bonded and nonbonded parameters from pdb2gmx. Did you have take a look in the top directory in GROMACS distrib?
This thread is closed for me since it is not an Amber problem.
Stéphane
________________________________________
De : roja rahmani [roja.rhmn.gmail.com]
Envoyé : mardi 30 janvier 2018 17:15
À : AMBER Mailing List
Objet : Re: [AMBER] Empty .frcmod file
but i face with;In the chosen force field there is no residue type for
'THR' as a starting terminus.
sorry you're right.
o k, i use this script
https://www.dropbox.com/s/rfjpz45we1f5h0z/amb2gmx_dihe_old.pl for
converting .prmtop to gromacs input files.
>> perl amb2gmx.pl --prmtop threonine.prmtop --crd threonine.inpcrd
--outname THRR
but thereis nothing in files as it says;
[roja.localhost cmd]$ perl amb2gmx.pl --prmtop threonine.prmtop --crd
threonine.inpcrd --outname THRR
sh: ambpdb: command not found
sh: rdparm: command not found
Parsing PDB file THRR.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.
-------------------------
sorry maybe i ask ask stupid questions, but i'm beginner
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 30 2018 - 10:00:02 PST
