[gmx-users] error in converting charmm to gromacs !!

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 29 17:42:45 CEST 2009

Chanchal wrote:
> Hi All,
>     I am have built a DOPC+water (tip3p) system in www.charmm-gui.org 
> <http://www.charmm-gui.org>. I converted *.itp file from CHARMM *.prm 
> file using Mark Abraham's script. I placed these *.itp files into the 
> GMXLIB directory. I have also edited FF.dat file and add a line 
> "ffcharmm CHARMM 27" and updated the line number. Now when I execute the 
> command:  /Users/parimalkar/gromacs-4.0.
> 5/bin/pdb2gmx_d -ff charmm -f step5_assembly.pdb -p topol.top, I got the 
> error message
> "Fatal error:
> Library file ffcharmm.atp not found in current dir nor in default 
> directories.
> (You can set the directories to search with the GMXLIB path variable)"
> Now when I copied the ffcharmm27.atp to ffcharmm.atp, and executed the 
> same command, then I got the error message:
> Program pdb2gmx_d, VERSION 4.0.5
> Source code file: resall.c, line: 138
> Fatal error:
> Atom type ON2b (residue TP1) not found in atomtype database
> But I saw that ffcharmm.rtp (Yuguang Mu's file that I got from Mark 
> Abraham) contains ON2b. So how can I fix this error? Is it problem with 
> ffcharmm.atp? Should I not copy ffcharmm27.atp to ffcharmm.atp?

The atomtype database is the .atp file, not the .rtp.  If the atom does not 
appear in the .atp file, you won't be able to use that type without defining 
parameters for it.


> Thanks
> Chanchal
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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