[gmx-users] error in converting charmm to gromacs
chanchal.kar at gmail.com
Tue Sep 29 02:43:55 CEST 2009
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Currently I am working on DOPC membrane simulation. I have built the
membrane in www.charmm-gui.org website. I am using Mark Abraham's charmm to
gromacs script 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).
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 someone shed light on it.
I placed these *.itp files into the direcotry:
/home/users/parimalk/software/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
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?
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