Hi!
I am using amberTools 1.0 patched with lastest bugfixes.
I have some small pdbs and I trying this:
cat >| sleap.in << EOF
source leaprc.ff03
source leaprc.gaff
set default fastbld on
X = loadpdb mypdb.pdb
saveamberparm X X.top X.xyz
quit
EOF
sleap -f sleap.in >| sleap.out
For one I got top and xyz, but all others, I got this:
[snip]
[gtkleap]$ X = loadpdb mypdb.pdb
basic_string::substr
and it failed.
What's wrong with my pdbs? At tleap they load fine.
And I tried to convert them to mol2 (via babel). Now all failed:
for item in `ls ???.pdb`; do
base=`basename $item .pdb`
mkdir -p $base
cd $base
\cp ../$item .
babel -ipdb $item -omol2 $base.mol2
cat >| sleap_$base.in << EOF
source leaprc.ff03
source leaprc.gaff
set default fastbld on
$base = loadmol2 $base.mol2
saveamberparm $base $base.top $base.xyz
quit
EOF
sleap -f sleap_$base.in >| sleap_$base.out
cd ..
done
Output for one case:
[snip]
[gtkleap]$ saveamberparm GGG GGG.top GGG.xyz
Error: unknown atom type N.am
These new functionalities in sleap are very cool, when it works.
Any help here would be very appreciated.
Many thanks in advance,
Alan
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Sun Jun 08 2008 - 06:07:12 PDT
