I ran ptraj as specified in the amber7 tutorial 'Generalized Born solvent
model' on a Linux server in Amber8.
The problem is that the pdb files that were generated had no charge
information, and since it is a non standard molecule amber does not have a
library file for it.
Following this i wrote a script to convert the pdb files to prepin format,
using the -c bcc option to generate the charges, then convert then back to
pdb (using -c bcc). The pdb files formed still have no charge information,
but the NEWPDB.PDB file generated does have the charge information.
So, i ask: Is PTRAJ supposed to put the charge information in the pdb file
and is antechamber able to write/generate charge information in to pdb files
with no library files.
The PTRAJ script i used is as follows:
ptraj trx.top
trajin bar.md.x
reference bar.crd
RMS reference out bar.rmsd
trajout MD_DATA/trx.pdb PDB
EOF
The scripts used to convert the pdb files to prepin and back to pdb are as
follows.
1) Done in a 2.8 GHz P4 with Amber7 running RedHat Enterprise3.0
for((i=1;i<=100;i++))
do
pdb_name="trx.pdb.$i"
prep_name="trx.prep.$i"
antechamber -i $pdb_name -fi pdb -o $prep_name -fo prepi
new_pdb="new.pdb.$i"
antechamber -i $prep_name -fi prepi -o $new_pdb -fo pdb
done
And
2) A 94 node, 194 CPU Linux Cluster based on Xeon 2.8 GHz cpus, running
Fedora Core 3.
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/mpich-1.2.5-i-gm/lib/shared
/usr/local/bin/mpiexec
for((i=1;i<=100;i++))
do
pdb_name="trx.pdb.$i"
prep_name="trx.prep.$i"
/usr/local/bin/mpiexec antechamber -i $pdb_name -fi pdb -o
$prep_name -fo prepi -c bcc
new_pdb="new.pdb.$i"
/usr/local/bin/mpiexec antechamber -i $prep_name -fi prepi -o
$new_pdb -fo pdb -c bcc
done
Any advice would be very much appreciated
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Received on Thu Mar 10 2005 - 06:53:00 PST
