[gmx-users] new version of C terminus database for charmm

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 23 15:58:14 CEST 2008

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 ]
[ 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.


> 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


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