AMBER Archive (2007)

Subject: Re: Re: AMBER: crd to pdb conversion

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Feb 19 2007 - 11:12:43 CST

Dear Aytug,

I am not familiar with the ALASCAN option of mm_pbsa. But you are saying
that the .crd files are created by mm_pbsa; that means that u have a
prmtop file. If that is the case, u can use that prmtop file (with the
.crd files) to create the .pdb files; and then change the atom names (the
mutated residues) to get your final .pdbs. I am not sure what else can
be done to get the .pdb files for these .crd coordinate files. Good luck.

Best,

On Mon, 19 Feb 2007, AYTUG TUNCEL wrote:

> Dear ilyas,
>
> Thanks for the information. Do you know a method for creating the prmtop files for the crd snapshots (those that have mutated residues) produced by mm_pbsl with ALASCAN option?
>
> Aytug
>
> -----Original Message-----
> From: Ilyas Yildirim <yildirim_at_pas.rochester.edu>
> To: <amber_at_scripps.edu>
> Date: Mon, 19 Feb 2007 08:35:16 -0500 (EST)
> Subject: Re: AMBER: crd to pdb conversion
>
> Dear Aytug,
>
> .crd files store only the coordinate information. Without knowing what the
> atoms are (which are stored in .prmtop file), there is not way you can
> create a .pdb file.
>
> On Mon, 19 Feb 2007, AYTUG TUNCEL wrote:
>
> > Dear all,
> >
> > Is there anyway converting the crd file to pdb format directly without the prmtop file. Because I used the ALASCAN in mm_pbsa module in order to create mutated residues but it requires new prmtop files for binding energy calculation. How can I create the new prmtop files for the corresponding structures that bear the mutated residues?Thanks in advance.
> >
> > Aytug
> >
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>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
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