sunita gupta wrote:
Hello Everyone
I am setting up a system for protein ligand complex using amber force
filed with Gromacs 4.5.
in pdb2gmx command i used -water tip3p
but when executing genbox command with -cs ffamber_tip3p.gro....I am
getting follwing error "*Fatal error:
Library file in current dir nor not found ffamber_tip3p.groin default
directories.
(You can set the directories to search with the GMXLIB path variable)*
Also I manually edited the complex.top file tip3p.itp ->
ffamber_tip3p.itp...still the problem persists
I searched the /gromacs-4.5/share/gromacs/top directory, and did not
find any such file there...
Can anyone please guide me where I can get ffamber_tip3p.gro file or
solve my problem?
There has been significant reorganization to the force field directories in
Gromacs 4.5. You can use any 3-point water box to do the solvation, i.e.
spc216.gro, since AFAIK no other 3-point water coordinate files are distributed
with Gromacs. The call to "ffamber_tip3p.itp" is also outdated. Look into the
new force field structure to get the proper call for your force field (i.e.
amberXX.ff/tip3p.itp).
-Justin
--
--
SUNITA GUPTA
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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