Re: [AMBER] antechamber ERROR

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 18 May 2011 15:18:28 -0400

Average PDBs are very often horrible starting structures for antechamber, since rotationally degenerate atoms are superimposed, and an average tends to be distorted for a QM starting structure.

Moreover, can't you reuse the prep or off files created for the original prmtop? If you don't, you won't get compatible charges for the original system.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On May 18, 2011, at 2:24 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi everybody,
> 
> I've generated an average pdb structure from a processed mdcrd file. I intend to use this average structure to generate topology files to visualise the processed trajectory.
> 
> The average structure is attached. It consists of a receptor, ligand and one water molecule (closest to the ligand).
> 
> I extracted from this average structure the ligand and save it as ligand pdb.
> 
> I then tried to generate a mol2 file by using the following command:
> 
> antechamber -i ligand.pdb -fi pdb -o bal.mol2 -fo mol2 -c bcc -s 2
> 
> I got the following error message
> 
> Warning: the assigned bond types may be wrong, please : 
> (1) double check the structure (the connectivity) and/or 
> (2) adjust atom valence penalty parameters in APS.DAT, and/or 
> (3) increase PSCUTOFF in define.h and recompile bondtype.c
>    Be cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time
> 
> Error: cannot run "/Users/gt/Programs/amber11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in judgebondtype() of antechamber.c properly, exit
> 
> I also tried the following.
> 
> Opened ligand.pdb in Chimera and save it as ligand2.pdb (This created new connectivities).
> 
> I re-run antechamber and got: 
> 
> Running: /Users/tzotzos/Programs/amber11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> Running: /Users/tzotzos/Programs/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> 
> Total number of electrons: 132; net charge: 0
> 
> Running: /Users/tzotzos/Programs/amber11/bin/sqm -O -i sqm.in -o sqm.out
> Error: cannot run "/Users/tzotzos/Programs/amber11/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
> 
> Your help in solving this problem will be greatly appreciated.
> 
> Best regards
> 
> George
> 
> <ligand.pdb>
> 
> 
> 
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Wed May 18 2011 - 12:30:02 PDT