Any suggestions on this topic? Thanks again for your time.
Dear Gromacs Users, > I am trying to find out the relative free energy difference of binding of > a ligand with wild type protein (Glutamate residue) and mutant protein > (Alanine residue). > > For charge part of the mutation, this is what I'm planning to do: > > ; residue 40 GLU rtp GLU q -1.0 > 552 opls_238 40 GLU N 191 -0.5 14.0067 > opls_238 -0.5 14.0067 ; qtot 0.5 > 553 opls_241 40 GLU H 191 0.3 1.008 > opls_241 0.3 1.008 ; qtot 0.8 > 554 opls_224B 40 GLU CA 191 0.14 12.011 > opls_224B 0.14 12.011 ; qtot 0.94 > 555 opls_140 40 GLU HA 191 0.06 1.008 > opls_140 0.06 1.008 ; qtot 1 > 556 opls_136 40 GLU CB 192 -0.12 12.011 > opls_135 -0.18 12.011 ; qtot 0.88 > 557 opls_140 40 GLU HB1 192 0.06 1.008 > opls_140 0.06 1.008 ; qtot 0.94 > 558 opls_140 40 GLU HB2 192 0.06 1.008 > opls_140 0.06 1.008 ; qtot 1 > 559 opls_274 40 GLU CG 193 -0.22 12.011 > opls_140 0.06 1.008 ; qtot 0.78 > 560 opls_140 40 GLU HG1 193 0.06 1.008 > DUM_140 0.0 1.008 ; qtot 0.84 > 561 opls_140 40 GLU HG2 193 0.06 1.008 > DUM_140 0.0 1.008 ; qtot 0.9 > 562 opls_271 40 GLU CD 194 0.7 12.011 > DUM_271 0.0 12.011 ; qtot 1.6 > 563 opls_272 40 GLU OE1 194 -0.8 15.9994 > DUM_272 0.0 15.9994 ; qtot 0.8 > 564 opls_272 40 GLU OE2 194 -0.8 15.9994 > DUM_272 0.0 15.9994 ; qtot 0 > 565 opls_235 40 GLU C 195 0.5 12.011 > opls_235 0.5 12.011 ; qtot 0.5 > 566 opls_236 40 GLU O 195 -0.5 15.9994 > opls_236 -0.5 15.9994 ; qtot 0 > > > I added the DUM_140, DUM_271,DUM_272 atomtypes in ffnonbonded.itp. > Further I added the bondtypes, angletypes and dihedraltypes in > ffbonded.itp for state B. > > In order to maintain the electroneutrality, I am mutating a K+ ion to > dummy as well. For the K+ going to dummy, I added a DUM_408 atomtype as > well. > > *The questions I have are as follows:* > *During the charge mutation will my dummy atoms have sigma and epsilon as > 0.0? Since Ala residue does not have Cgamma, Cdelta and the oxygen as well > as the Hgamma, all the dummy atoms should have sigma and epsilon as zero. > Am I correct for this assumption?* > *Further as I am mutating one ion, I dont want the mutating ion to come > close to other ions (I have three K+ ions as my protein has -3 charge) as > well as the protein atoms. Hence I'm having position restraints on the > three ions. * > *For the ion that is mutating to dummy, should I have have position > restraints on dummy atom as well for the B state topology?* > > The section of topology for the K+ going to dummy is as follows: > > [ moleculetype ] > ; Name nrexcl > KM 1 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass typeB > chargeB massB > 1 opls-408 1 KM KM 1 1 39.0983 > DUM_408 0.0 39.0983 > > #ifdef POSRES_ION > ; Position restraint for each Potassium ion > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 0 0 0 > #endif > > Here I defined the KM as K+ that will go to dummy and other two K+ ions > are represented as regular K+ ions. > I'm pasting the regular K+ ion part of the topology below. > > [ moleculetype ] > ; Name nrexcl > K 1 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass typeB > chargeB massB > 1 opls_408 1 K K 1 1 39.0983 > > #ifdef POSRES_ION > ; Position restraint for each Potassium ion > [ position_restraints ] > ; i funct fcx fcy fcz > 1 1 1000 1000 1000 > #endif > > Let me know if you need more information. > > Thanks for your time, > > Regards > Sai > >
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