Re: [AMBER] Two questions about Net charge and write frcmod in parmed.py

From: Arun Srikanth <askforarun.gmail.com>
Date: Thu, 18 Sep 2014 14:32:16 -0400

Thanks jason.
I am attaching the mol2, topology file and the resulting frcmod file which
I obtained using write frcmod command. Please have a look

I have two other questions:

1. I am creating a bond between two atoms. This bond is introducing new
angles, dihedrals. I need to know what unique type of new angles and
dihedrals this bond introduces in the system.

Can this be done using parmed.py and is there any neater way ?

2. What is the meaning of the string "M" and "I" that is printed on the
left most corner when printdihedrals command is issued in parmed.py

Thanks for your help
Arun



On Thu, Sep 18, 2014 at 7:29 AM, Jason Swails <jason.swails.gmail.com>
wrote:

> On Wed, 2014-09-17 at 21:36 -0400, Arun Srikanth wrote:
> > Hello. I have two questions,
> >
> > First question:
> >
> > I have calculated the partial charges using am1bcc for the atoms in my
> > molecule (from antechamber). I generated the topology file from the mol2
> > file from leap. But when I check the netcharge using parmed.py. It is not
> > zero.
> >
> > It is showing a value of -0.001 for the molecule. Can this be neglected
> > during a simulation. I am simulating a bulk system so this charge
> (-0.001)
> > scaled by the system size is giving a warning in my simulation.
>
> Yes, you can ignore this. If you wanted to, you could add a charge of
> 0.001 to one of the atoms in your mol2 file to force it to be neutral
> (or you can spread that 0.001 out across several atoms -- it's so little
> charge that it won't make a noticeable difference).
>
>
> > Second question:
> >
> > When I use the write Frcmod to see the parameters defined in the topology
> > file. It shows that the bond coefficients are defined multiple times.
> For
> > eg
> >
> > ca - c3
> > c3 - ca
> >
> > both have the same coefficients.
> >
> > I need unique bond types from write Frcmod. I can write script to get the
> > unique bond types but is there any other way ?
>
> I wasn't aware that it printed duplicates. What version of AmberTools
> are you using? Can you send me the example topology file so I can check
> it?
>
> Thanks,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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> AMBER.ambermd.org
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>


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Received on Thu Sep 18 2014 - 12:00:02 PDT
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