Hi, everybody!
I tried to run a simple MD simulation with the charmm ff in nwchem 6.8 and 6.6.
But I get strange errors (see below for input and output) when trying to prepare the system: missing parameters for the protein residues even though these parameters are listed in the charmm.par file.....
Did anybody tested charmm ff in nwchem 6.8 or 6.6?
Can she/he provide me with some test files?
Thanks in advance!
Best,
Martin
Input:
- This is a AMBER test that uses a PDB geometry, and the *.frg files from NWChem to asign atom types
Title "big"
memory 3500 Mb
permanent_dir .
echo
prepare
system big
source big.pdb
new_top new_seq
new_rst
solvent name HOH model TIP3
end
print debug
task prepare
Output (last lines):
Number of atom types is 25
Parameter file /opt/nwchem-6.8/src/data/charmm_s/charmm.par
pre_ffield done
Undetermined force field parameters
Parameters could not be found for bond type NH3 -HC ( N -2H )THR_N 1 1 2 1 1 0
Parameters could not be found for bond type NH3 -CT1 ( N - CA )THR_N 1 1 5 4 1 0
Parameters could not be found for bond type CT1 -OH1 ( CB - OG1 )THR_N 1 7 9 9 1 0
Parameters could not be found for bond type OH1 -H ( OG1 - HG1 )THR_N 1 9 10 11 1 0
Parameters could not be found for bond type C -O ( C - O )THR_N 1 15 16 15 1 0
Parameters could not be found for bond type C -NH1 ( C - N )THR_N 1 15 17 16 1 0
Parameters could not be found for bond type NH1 -H ( N - H )GLU 2 17 18 17 1 0
Parameters could not be found for bond type NH1 -CT1 ( N - CA )GLU 2 17 19 18 1 0
Parameters could not be found for bond type CC -OC ( CD - OE1 )GLU 2 27 28 28 1 0
Parameters could not be found for bond type CC -O ( CD - OE1 )GLN 4 57 58 58 1 0
Parameters could not be found for bond type CC -NH2 ( CD - NE2 )GLN 4 57 59 59 1 0
Parameters could not be found for bond type NH2 -H ( NE2 -2HE2 )GLN 4 59 60 60 1 0
Parameters could not be found for bond type CT2 -NH3 ( CE - NZ )LYS 9 141 144 145 1 0
Parameters could not be found for bond type CT2 -OH1 ( CB - OG )SER 13 199 202 204 1 0
Parameters could not be found for bond type NH1 -CT2 ( N - CA )GLY 19 291 293 295 1 0
Parameters could not be found for bond type CT2 -S ( CG - SD )MET 32 478 481 484 1 0
Parameters could not be found for bond type S -CT3 ( SD - CE )MET 32 481 482 485 1 0
Parameters could not be found for bond type CT2 -NC2 ( CD - NE )ARG 33 498 501 504 1 0
Parameters could not be found for bond type NC2 -HC ( NE - HE )ARG 33 501 502 505 1 0
Parameters could not be found for bond type NC2 -C ( NE - CZ )ARG 33 501 503 506 1 0
Parameters could not be found for bond type C -N ( C - N )ASN 38 578 580 582 1 0
Parameters could not be found for bond type N -CP1 ( N - CA )PRO 39 580 581 583 1 0
Parameters could not be found for bond type N -CP3 ( N - CD )PRO 39 580 583 584 1 0
Parameter file contains these parameter, e.g.
NH3 -HC 0.10400 3.37230E+05
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