Thank you Jason,
But let me see if I understood well.
I moved the library and forcefield files generated for the original ligand.prmtop to a new directory. These files are:
ligand.frcmod
ligand.lib
sqm.in
sqm.out
I also moved in the same directory the ANTECHAMBER* files as well as the ligand.mol2 file generated by ANTECHAMBER originally.
I started tleap:
tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
source leaprc.gaff
set default PBradii mbondi2
Loaded the NEW protein pdb (protein+WAT) and saved the parameter files
Did the same for the complex (protein+WAT+Ligand).
I then tried to visualise
LIGAND=loadmol2 ligand.mol2
In both cases I got some 430 warnings of the type:
WARNING: There is a bond of 0.371657 angstroms between:
------- .R<LYS 124>.A<CD 11> and .R<LYS 124>.A<HD2 12>
WARNING: There is a bond of 0.359783 angstroms between:
------- .R<LYS 124>.A<CD 11> and .R<LYS 124>.A<HD3 13>
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 437 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
====================================
Needless to say that when I used the generated complex.prmtop file to visualise the PROCESSED trajectory, the result was ..... shall we say disappointing.
Sorry to bother you with this but I'm rather stuck.
Have a good evening
George
On May 18, 2011, at 9:49 PM, Jason Swails wrote:
> You can use the average PDB, just make sure you use the same library files
> and force field files for the new leap script as you did for the original
> one when you built the system in the first place.
>
> That is, there is *no* need to re-run antechamber (just use the results from
> the first time you ran it).
>
> HTH,
> Jason
>
> On Wed, May 18, 2011 at 9:27 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> 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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>>>
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed May 18 2011 - 14:00:03 PDT
