Many thanks Jason.
Below is the script I used to process the original trajectory files.
closest.in
trajin prod_2ns.mdcrd
trajin prod_4ns.mdcrd
trajout prod_closest_WAT.mdcrd
center :1-142
image familiar
solvent byres :WAT
closest 1 :142
strip :Na+
average aver.pdb pdb
Is there better way of generating a prmtop files for <closest_WAT.mdcrd> ?
I understand that I should use these new files (ligand.prmtop; protein/WAT.prmtop; protein/WAT/ligand.prmtop) with MMPBSA.py
Many thanks for your advice
George
On May 18, 2011, at 9:18 PM, Jason Swails wrote:
> 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>
>>
>>
>>
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Received on Wed May 18 2011 - 12:30:03 PDT
