AMBER Archive (2003)

Subject: AMBER: Re: initial structures

From: Raghunadha Reddy Burri (burri_at_heineken.chemie.uni-dortmund.de)
Date: Mon Dec 08 2003 - 11:19:10 CST

Thanks for reply,
I want use this pdb file to GROMACS simulation. I am looking for structure
look like SWISS-MODEL Protein Modelling (with one helices), I hope this is
"native" structure.

please give me some details to use "impose".

Bye
Raghu Burri

On Monday 08 December 2003 16:51, Carlos Simmerling wrote:
> Do you want a starting structure that is acceptable,
> meaning simulations will not crash, or do you want
> a good guess for the "native" structure? these are different
> questions with very different answers.
>
> also, please be more specific as to what you mean by
> the leap structure "view not good".
> we can't help unless we know the details of the problem.
> carlos
>
> ----- Original Message -----
> From: "Raghunadha Reddy Burri" <burri_at_heineken.chemie.uni-dortmund.de>
> To: <amber_at_scripps.edu>
> Sent: Monday, December 08, 2003 10:21 AM
> Subject: AMBER: initial structures
>
> > Dear Users,
> > I am very new to this group, I have a peptide sequence with 42 residues.
> > I
>
> am
>
> > looking for starting structure in the form of a pdb file. I used LEaP to
> > build the but I got a pdb file which structure view not good,
> > any wrong in my process? please give some more suggestions to get good
>
> AMBER
>
> > force field.
> >
> > Any suggestion are welcome
> >
> > Thanks for your time and consideration, please check my file
> >
> >
> > ______________________________________________
> >
> > #!/bin/sh
> >
> > #------------------------------------------------------
> > # Build Forcefiled
> > #------------------------------------------------------
> >
> > LEAPROOT=/pc2a/burri/LEAP
> >
> > #
> > cat > pep.lep <<EOF
> > #
> > parm94 = loadAmberParams "parm94.dat"
> > loadOff all_amino94.lib
> > loadOff all_aminont94.lib
> > loadOff all_aminoct94.lib
> >
> > U=sequence{ ASP ALA GLU PHE ARG HIS ASP SER GLY TYR GLU VAL HIS HIS GLN
>
> LYS
>
> > LEU VAL PHE PHE ALA GLU ASP VAL GLY SER ASN LYS GLY ALA ILE ILE GLY LEU
>
> MET
>
> > VAL GLY GLY VAL VAL ILE ALA }
> >
> > pep=sequence { ACE U NME }
> >
> > saveamberparm pep pep.top pep.crd
> > saveoff pep pep.off
> > savepdb pep pep.pdb
> > quit
> > EOF
> >
> > tleap -f pep.lep
> > ______________________________________________
> >
> >
> > looking for reply
> >
> > Yours
> > Raghunadha Reddy Burri
> >
> >
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