Hi Audrius,
I personally strongly recommend against manual editing of parm files. I
believe I am not alone in that opinion. However, Jason Swails recently
released a parm editing utility with AmberTools12 called parmed.py. It
still requires a bit of familiarity with the parm format, but seems to be
much safer and robust than manual editing.
As for your actual question, yes, but you must be very careful. This is
because the A and B parameters are assigned by type, not by atom (so if you
count the entries you will have N*(N+1)/2 where N is NTYPES not NATOMS).
Assuming that there are many atoms of the type that you are disappearing,
you cannot do it trivially. If there is just one, you are in luck! In the
former case you would probably have to add unique types for each of the
atoms to be disappeared and *then* use parmed to make a series of parm
files in which the parameters go to zero. Although, if you are already
mucking around with frcmods, etc. you might consider bypassing parmed
altogether.
Jason might have a better idea and obviously has a better grasp of what
parmed is capable of; hopefully he will have some useful comments to add.
Regards,
Brian
On Fri, May 25, 2012 at 7:16 AM, Audrius Laurynėnas <
audrius.laurynenas.gmail.com> wrote:
> Dear Amber users,
>
> I have some questions about manual editing prmtop files for free energy
> calculations. In prmtop file exists some lines with flags:
>
> %FLAG LENNARD_JONES_ACOEF
>
> %FORMAT(5E16.8)
>
> %FLAG
> LENNARD_JONES_BCOEF
> %FORMAT(5E16.8)
>
> My question is if I change approprietely Lennard_Jones coefficients in
> these lines, do i get same free energy of turning off van der Waals for
> solvent in solution, as in calculation with dummy atoms?
>
> Thank you for answers in advance.
>
> Audrius
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Received on Fri May 25 2012 - 06:30:04 PDT
