sarbani chattopadhyay wrote:
Hi,
I am trying to run gromacs with charmm forcefield.
# I had run the perl program "convert_charmm_to_gromacs.pl" and put the
output files
"ffcharmmbon.itp" and "ffcharmmnb.itp" into the gromacs
share/gromacs/top directory.
# I had put all the files from the "tar" file into the share/gromacs/top
directory.
# I had updated the "FF.dat" file to include the charmm file.
# I undersatand that the format of the termini database have changed for
the 3.3.2 version.
I could make the changes in "ffcharmm-n.tdb".
Accordingly I tried to make the changes in "ffcharmm-c.tdb", but when I
give the command
pdb2gmx -f 1aoc.gro -ff charmm -ter
I get the following error
Reading Termini Database: expected 3 items of atom data in stead of 1 on
line
O OC 15.9994 -0.670
I guess the ffcharmm-c.tdb file has not been changed correctly.Has
anyone done it?
I will be grateful if someone can help me in this.
This was a strange error; I remember coming across it as well. No modification
that I could make to that line alleviated the problem, and I still don't know
why. What I ended up doing was changing the [ COO- ] section to the following:
[ COO- ]
[ replace ]
C CC 12.0110 0.340
[ add ]
2 8 O C CA N
OC 15.999 -0.670
[ delete ]
O
[ impropers ]
C CA O2 O1 improper_OB_X_X_CD_
Therefore, instead of replacing O by OC, the O is deleted, and an OC added back
in its place. I don't know why that works, and the "replace" function doesn't,
so maybe someone else has a better idea, but this is how I got around it.
-Justin
Thanks in advance
Sarbani
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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