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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On May 25, 2012, at 11:17 PM, Brian Radak <radak004.umn.edu> wrote: > 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 >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > > > -- > ================================ Current Address ======================= > 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 > ==================================================================== > Sorry for the multiple e-mail addresses, just use the institute appropriate > address. > _______________________________________________ > 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/amberReceived on Sun May 27 2012 - 04:00:03 PDT