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.
-Justin
Thanks
Chanchal
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
