AMBER Archive (2008)

Subject: AMBER: problems with sleap

From: Alan (alanwilter_at_gmail.com)
Date: Wed Jun 04 2008 - 10:40:04 CDT

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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