[gmx-users] Library file ffamber_tip3p.gro not found in current directory

[Justin A. Lemkul]

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  The call to "ffamber_tip3p.itp" is also outdated.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
> 

-- 
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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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