AMBER Archive (2009)

Subject: Re: [AMBER] Protein with HETATM, am I doing the right thing

From: nicholus bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Thu May 21 2009 - 11:28:52 CDT

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

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