Dear David,
Sorry for posting the message twice. Anyway I am running
the antechamber before leap. I am attaching my original pdb file (named pdb
which contains HETATM PO4). So while loading this in leap it shows unknown
residue PO4.
So coppy the HETATM part in a file named po4. Then I run the antechamber as
follows
$ antechamber -i po4 -fi pdb -o po4.prepin -fo prepi -c bcc -s 2 -c -3
(don't know any other charge value for PO4)
It gave the folloging message
Info: Bond types are assigned for valence state 1 with penalty of 1
Running: /usr/local/amber9/exe/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Running: /usr/local/amber9/exe/atomtype -i ANTECHAMBER_PREP.AC0 -o
ANTECHAMBER_PREP.AC -p gaff
Running: /usr/local/amber9/exe/prepgen -i ANTECHAMBER_PREP.AC -f int -o
po4.prepin -rn "PO4 " -rf molecule.res
It generated the following files
ANTECHAMBER_BOND_TYPE.AC ANTECHAMBER_PREP.AC0
ANTECHAMBER_AC.AC ANTECHAMBER_BOND_TYPE.AC0 ATOMTYPE.INF
po4.prepin
ANTECHAMBER_AC.AC0 ANTECHAMBER_PREP.AC NEWPDB.PDB
PREP.INF
Then I run the following command
$ parmchk -i sustiva.prepin -f prepi -o sustiva.frcmod
After that I entered the leap through tleap command
I sourced both leaprc.gaff and leaprc.ff99SB
then
> loadamberprep po4.prepin
Now when I load my pdb file named pdb no unknown residue is shown. After
solvating and charge neutralization it could generate the parameter and
coordinate files which was not possible earlier. All I want to know that am
I following the right path for proteins with heteroatoms present in them.
- application/octet-stream attachment: pdb
- application/octet-stream attachment: po4
Received on Fri May 22 2009 - 01:07:32 PDT
