Re: Re: [AMBER] ligand-protein complex parametrization problems

From: case <>
Date: Fri, 12 Mar 2010 08:08:57 -0500

On Fri, Mar 12, 2010, Andrew Voronkov wrote:

> I have of course used antechamber and parmchk to get prepin and
> frcmod(showed below), otherwise I wouldn't post this. Sorry, I haven't
> mentioned it (as obvious).

> > > Building bond parameters.
> > > Could not find bond parameter for: cf - br

Something is going on that is not evident from what you have posted. The
prepin file you posted doesn't have any atoms of type "cf" (as an example).
If I use the following commands, with the files you provided, everything is

poincare% tleap -f leaprc.gaff
-I: Adding /home/case/amber11/dat/leap/prep to search path.
-I: Adding /home/case/amber11/dat/leap/lib to search path.
-I: Adding /home/case/amber11/dat/leap/parm to search path.
-I: Adding /home/case/amber11/dat/leap/cmd to search path.
-f: Source leaprc.gaff.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: /home/case/amber11/dat/leap/cmd/leaprc.gaff
Log file: ./leap.log
Loading parameters: /home/case/amber11/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic mol., add. info. at the end (June, 2003)
> loadAmberParams frcmod
Loading parameters: ./frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> loadAmberPrep
Loading Prep file: ./
> list
RES gaff
> saveAmberParm RES prmtop inpcrd


Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
 (no restraints)
> quit

So: I may have misread the problem statement; you may have posted the wrong
files(?); you may have something else loaded that has a "cf" atom type, etc.

At this point, I think you should start over and post again the input files
you used, the tleap commands you used, and the error messages you received.


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Received on Fri Mar 12 2010 - 05:30:03 PST
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