AMBER Archive (2003)

Subject: Re: AMBER: initial structures

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Dec 08 2003 - 09:51:04 CST

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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