[gmx-users] error in converting charmm to gromacs

Mark Abraham Mark.Abraham at anu.edu.au
Tue Sep 29 03:10:43 CEST 2009

Chanchal wrote:
 > Hi Mark,
 >   Sorry for off-the-list email. Actually I sent an email to the list 
but due the large size it is not sent.
 >  Currently I am working on DOPC membrane simulation. I have built the 
membrane in www.charmm-gui.org <http://www.charmm-gui.org/> website. I 
am using your scripts  to convert par_all27_prot_lipid.prm to 
charmmbon.itp and charmmnb.itp. When I tried the script 
convert_charmm_to_gromacs.pl (version 1.2) on par_all27_prot_lipid.prm I 
got the message "Sin of delta not zero, hope this is the only dihedral of
 >  type     X    CS    SS     X
 >  (sin delta = 0.00349065141522373).

The documentation inside my scripts deal with this. The warning message 
is normal.

 > I found that ffcharmmnb.itp has only 40 line starting with Cs and 
ends with HT. There are no entries for any atom types other than carbon
 > and hydrogen. Is it correct? Please find attached *.itp. Please 
someone shed light on it.

It may be correct - I can't be sure of the contents of the input file. 
If it only had these lipid atom types, then the results are correct. If 
it had other types, then the behaviour looks to be erroneous. Also, what 
version of my script were you using?

 >  I placed these *.itp files into the direcotry: 
 > gromacs-4.0.5/share/gromacs/top. Then I executed the command: 
pdb2gmx_d -ff charmm -f step5_assembly.pdb -p topol.top to create the 
topology .
 > I got the error message : Program pdb2gmx_d, VERSION 4.0.5
 > Source code file: futil.c, line: 527
 > Fatal error:
 > Library file ffcharmm.rtp not found in current dir nor in default 
 > (You can set the directories to search with the GMXLIB path variable)
 > How can I get the ffcharmm.rtp file?? I was looking  gromacs archives 
and the link given there is not working now. Can someone help me to fix 
this error and provide the *.rtp file?

Per my documentation, I don't provide an .rtp file, since I've never 
written one. Yuguang Mu's CHARMM port did provide one, and the 
not-really-supported CHARMM port in GROMACS 4.0.5 also provides one. In 
all cases, as I posted on gmx-users just yesterday, one needs to edit 
${GMXLIB}/FF.dat to have a line for CHARMM and update the total number 
of force fields available.


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