AMBER Archive (2009)

Subject: Re: [AMBER] How to build reference coordinate file for targeted MD

From: xiaonan zhang (heptoking_at_gmail.com)
Date: Thu Feb 05 2009 - 06:00:38 CST

Thank you very much Dr. Simmerling
You are always very helpful!!

Cheers ...

Xiaonan

On Thu, Feb 5, 2009 at 7:19 PM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> if they are the same protein sequence but different atom order in side
> each residue, leap will fix that.
> for the water molecules you might need to manually adjust the buffer
> size until you get the number from before.
>
>
>
>
> On Thu, Feb 5, 2009 at 1:44 AM, gmail <heptoking_at_gmail.com> wrote:
> > Dear All
> > I am trying to do a targeted MD for a big protein. There is a question
> on how to build a reference
> > coordinate file. As the manual pointed out that the reference coordinate
> are expected to match the prmtop
> > file of the starting structure. However, the starting and final
> structures are two different pdb files,
> > which although have the same amino acid sequence, the exact atom sequence
> are somewhat different. In addition,
> > I am thinking that if I create the solvated reference prmtop and inpcrd
> files, the number of water molecules
> > will be slightly different to those generated with starting pdb file.
> That will most probably cause failure of
> > recognition.
> >
> >
> > With no definite solution in my mind, I have to ask experts for
> suggestions.
> >
> >
> > Thank you in advance.
> >
> >
> > Cheers!
> >
> >
> > Xiaonan Zhang
> >
> > Shanghai public health clinical center
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber