Dear Amber community,
We try to calculate the relative binding free energy of ligand A and
B. The only difference between them is A:@CL1 & B:@BR1. After carefully
reading the Amber 14 manual and the pmemd.MPI paper (
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3811123/), I am still not 100%
sure if the following commands and prmtop are correct. Could any guru
kindly give some comments? Thanks!
Input File
Step1: Removing charge on A:.CL1
Step2: Changing A:.CL1 to B:.BR1
Step3: Adding charge on B:@BR1
pmemd.MPI
No group file needed
icfe = 1,
ifsc=0,
timask1=':1',
timask2=':2,
crgmask=’ :2.CL1’,
icfe = 1,
ifsc=1,
timask1=':1',
scmask1=':1.CL1',
timask2=':2', scmask2=':2.BR1',
crgmask=’ :1.CL1| :2.BR1’
icfe = 1,
ifsc=0,
timask1=':1',
timask2=':2,
crgmask=’ :1.BR1’,
prmtop
2 compound A + solvents
1 compound A + 1 compound B + solvents
2 compound B + solvents
One step transformation
Input File
Step1: Transform charge and vdw
pmemd.MPI
No group file needed
icfe = 1,
ifsc = 1,
timask1=':1', timask2=':2', scmask1=':1.CL1',
scmask2=':2.BR1',
crgmask=':1.CL1|:2.BR1',
prmtop
1 compound A + 1 compound B + solvents
Cheers,
Henry
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Received on Fri Nov 14 2014 - 15:00:02 PST
