[AMBER] pmemd.MPI thermodynamic integration (TI) relative binding free energy set up

From: <psu4.uic.edu>
Date: Fri, 14 Nov 2014 16:32:49 -0600

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
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