AMBER Archive (2003)

Subject: AMBER: initial structures

From: Raghunadha Reddy Burri (burri_at_heineken.chemie.uni-dortmund.de)
Date: Mon Dec 08 2003 - 09:21:28 CST

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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