Re: [AMBER] Dummy atom and PMEMD

From: Ali M. Naserian-Nik <naseriannik.gmail.com>
Date: Fri, 31 Aug 2012 11:50:57 +0430

To add two non-bonded dummy atoms I do the following steps:

1- First make a library file containing the dummy atom information (like
the file dh.lib attached) 2- Modify the PDB file by adding lines such this

TER

ATOM 761 DH DHA 25 3.109 11.283 -12.000 1.00 0.00
DH

TER

ATOM 762 DH DHA 26 16.137 -28.812 120.000 1.00 0.00
DH

TER

3- Load the dh.lib and modified PDB files into tleap and create a new
library file such as du2.lib. 4- Modify the du2.lib by adding the missed DH
names in this file.

5- Create a modified force field file, du.frcmod file, in which only the
mass of dummy atom is non-zero (please, see attachment).

6- Load the modified force field and du2.lib files into tleap and add
solvate box to the system.

7- Finally, I create the topology and coordinate files (I attach the
created topology file).


Is there any thing wrong?


The error massage which pmemd stop working with it, when the model is made
by above steps is:



| ERROR: PMEMD does not support single H residues!

| Atom number 761, Residue number 25


Thank you.



On Fri, Aug 31, 2012 at 12:35 AM, Jason Swails <jason.swails.gmail.com>wrote:

> On Thu, Aug 30, 2012 at 3:21 PM, Ali M. Naserian-Nik
> <naseriannik.gmail.com>wrote:
>
> > Dear Jason,
> >
> >
> >
> > Thank you for reply. I have added the non-bonded dummy atoms to the
> > topology file and do some SMD simulations vi sander without any problems.
> >
>
> How did you add them?
>
>
> > Nevertheless, the problem is with pmemd. Does the way you suggested for
> > adding the dummy atom enable pmemd to support simulations with the dummy
> > atoms?
> >
>
> What are the error messages? pmemd has better error checking on the whole
> than sander does, so if something is running with sander but not pmemd due
> to changes in the topology file, my guess is something is wrong and you
> don't know it.
>
> My suggestions should work in pmemd, but the error messages contain the
> best clues.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Fri Aug 31 2012 - 00:30:02 PDT
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