Generating *.mcf file with Gromacs *.itp file

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7 years 8 months ago - 7 years 8 months ago #230 by Zarathustra
Hello,

I am trying to generate an spce.mcf file for a simulation in Cassandra using a GROMACS force field file and am running into an error. I am using the spce.pdb from the NPT example file provided with CassandraV1.2 and I am using the spce.itp file provided by GROMACS. I have copy and pasted both files below this message as well as attached a *.tar.gz file. Here is what I get when I try running mcfgen.py from the command line

$ python mcfgen.py spce.pdb -f spce.itp


*********Generation of Topology File*********

Summary:
There are 2 bonds identified.
There are 0 rings identified. These rings are:
There are 1 fragments identified
There are 1 angles identified
There are 0 dihedrals identified
Reading Modified PDB File...
Traceback (most recent call last):
File "mcfgen.py", line 1564, in <module>
readGromacs(ffFile, atomParms, {}, {}, {}, {})
File "mcfgen.py", line 1186, in readGromacs
index = (int(data[0]), int(data[1]), int(data[2]))
ValueError: invalid literal for int() with base 10: '#endif'

In this particular case I could generate the *.mcf file by generating the FFtemplate and manually filling in the parameters, or I could even just us the spce.mcf file in the example, but in the future I would like to be able to use more complicated molecules which don't have *.mcf files already generated.

I appreciate any suggestion.

Thanks

Braden

spce.pdb:
ATOM 1 O1 X 1 0.776 0.790 0.000 0.00 0.00 O
ATOM 2 H2 X 1 1.776 0.791 0.000 0.00 0.00 H
ATOM 3 H3 X 1 0.442 1.733 0.000 0.00 0.00 H
END
CONECT 1 2 3
CONECT 2 1
CONECT 3 1
spce.itp:
[ moleculetype ]
; molname nrexcl
SOL 2

[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_116 1 SOL OW 1 -0.8476
2 opls_117 1 SOL HW1 1 0.4238
3 opls_117 1 SOL HW2 1 0.4238

#ifndef FLEXIBLE
[ settles ]
; OW funct doh dhh
1 1 0.1 0.16330

[ exclusions ]
1 2 3
2 1 3
3 1 2
#else
[ bonds ]
; i j funct length force.c.
1 2 1 0.1 345000 0.1 345000
1 3 1 0.1 345000 0.1 345000

[ angles ]
; i j k funct angle force.c.
2 1 3 1 109.47 383 109.47 383
#endif
Attachments:
Last Edit: 7 years 8 months ago by Zarathustra. Reason: Added *.tar.gz file

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