Re: [AMBER] Thermodynamic Integration using PMEMD

From: Roma Mukhopadhyay <>
Date: Fri, 18 Aug 2017 16:13:46 +0000


Attached is the zipped folder containing the pdb file, the prmtop. the incpcrd, the minimization input file and the minimization output file.

Here is a brief discussion of my problem:

I have a pdb file containing two molecules that are separated by TER card. The numbering based on pdb file shows molecule 1 has 25 atoms, and molecule 2 has 25 atoms.

Using leap I have generated a single prmtop and inpcrd files.

Then I try to run minimization on it. The ti mask i have applied is "timask1=':1',timask2=':2' ". However my output file generates this information:

 Energy averages sample interval:
| ene_avg_sampling = 1
     TI Mask 1 :1; matches 6 atoms
     TI Mask 2 :2; matches 13 atoms
     TI region 1: 37 atoms
     TI region 2: 44 atoms
     Checking for mismatched coordinates.
     ERROR: timask1/2 must match the same number of atoms for non-softcore run

since I have 25 atoms for each molecule , what I expected was TI Mask1:1, to match 25 atoms and the same with TI Mask2. Am I wrong in expecting that.

How do I take care of this error? Does this error have to do anything with the way my pdb file currently is?

Any and all help will be appreciated.


From: Hannes Loeffler <>
Sent: Friday, August 18, 2017 2:20:10 PM
Subject: Re: [AMBER] Thermodynamic Integration using PMEMD

On Fri, 18 Aug 2017 13:34:32 +0000
Roma Mukhopadhyay <> wrote:

> Hi,
> I did go through the A9 tutorial, and got the idea of how to setup
> the pdb file.

You may want to look into the side-chain mini tutorial if you are going
to use that on anything sizeable.

> So I had created the pdb file containing both molecules separated by
> TER card.

>From your leap script I guess you mean the output you created with
leap. That is of no relevance to pmemd.

> Then I got the single prmtop and inpcrd file using the
> tleap. Each molecule has 25 atoms, however when I run minimization,
> the program is recognizing 50 atoms of one atom, instead of
> recognizing 25 atoms for each molecule.

How did you determine that and why is that of relevance?

> In my minimization steps i did use timask flags.

But you don't tell us to what you have set it?

> How do I overcome this problem?

If you really want to get help with that you have to provide
considerable more information than what you have done so far. Give all
relevant input and output that you have used/created to get to the stage
where you are right now. You need to provide this in a way that anyone
on this list can follow your workflow. When you provide any files,
package them in some archive file (zip, tar) as it can be very
inconvenient to download multiple files through an email client.

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Received on Fri Aug 18 2017 - 09:30:02 PDT
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