Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI

From: Daniel Mermelstein <>
Date: Thu, 16 Jul 2015 16:42:12 -0700

Hi Olivia,

I think the problem is that if you don't use the softcore potentials
(ifsc=0), then you need to add dummy atoms into TI mask 2. This is so you
don't have singularities or extremely unfavorable repulsive interactions
when your atoms "come into existence" so to speak.

So you can try one of two things. You can run with softcore potentials
(ifsc=1) or you can add dummy atoms into TI Mask 2.

Hope that helps!

Dan Mermelstein

On Thu, Jul 16, 2015 at 3:13 PM, M Olivia Kim <> wrote:

> Hi,
> I am trying to run a FEP simulation for mutation of a protein residue
> using the pmemd.MPI module. I'm mutating a Phe to Ala - following the
> Amber14 manual, I prepared the prmtop and inpcrd files using
> where the redundant bonding terms for the overlapping residues are deleted.
> So the final pdb for my system looks like that protein consists of residues
> 1-177 and the residues 178 is Ala (separated by TER), which is the mutant
> for the Phe in the WT.
> I was first trying to run the non-soft core simulation, where the atomic
> charges of the WT protein residue are changed to the charges of the mutated
> residue along with lambda. However, since the atom numbers of the WT
> residue and mutant are different, I couldn't even run the minimization. The
> part corresponding to TI in my minimization input file is:
> icfe = 1, clambda = 0.0,
> ifsc = 0,
> timask1 =
> '.1019,1020,1021,1022,1023,1024,1025,1026,1027,1028,1029,1030,1031,1032,1033,1034,1035,1036,1037,1038',
> timask2 = '.2780,2781,2782,2783,2784,2785,2786,2787,2788,2789',
> crgmask = '.2780,2781,2782,2783,2784,2785,2786,2787,2788,2789',
> /
> And the error message I got is:
> TI Mask 1
> .1019,1020,1021,1022,1023,1024,1025,1026,1027,1028,1029,1030,1031,1032,1033,1034,1035,1036,1037,1038;
> matches 20 atoms
> TI Mask 2 .2780,2781,2782,2783,2784,2785,2786,2787,2788,2789; matches
> 10 atoms
> ...
> ERROR: timask1/2 must match the same number of atoms for non-softcore run
> Is there any way I can correct my input or prmtop file so that I can run
> this simulation? Or is this type of simulation (mutation of a protein
> residue to another that has different number of atoms) not supported by
> pmemd version of TI in Amber yet? I'll look forward to any advice or
> comments. Thanks in advance!
> Best,
> Olivia
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Received on Thu Jul 16 2015 - 17:00:03 PDT
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