AMBER Archive (2009)

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

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu May 21 2009 - 07:39:14 CDT

On Thu, May 21, 2009, nicholus bhattacharjee wrote:

> My protein contains HETATM PO4. Since these residues are not
> recognized by in leap I used antechber in the following way.
>
> 1. Made a file of HETATM po4 (filename).
> 3. tleap
> 4. source leaprc.gaff
> 5. source leaprc.ff99SB
> 6. antechamber -i po4 -fi pdb -o po4.prepin -fo prepi -c bcc -s 2 -c -3
> 7. parmchk -i po4.prepin -f prepi -o po4.frcmod
> 8. mol=loadpdb pdb(main pdb file)

First: there is no need to post the same question twice within an eight-hour
period.

Second, you should run antechamber and parmchk outside of tleap, not as a
command inside it as you seem to be doing above.

Third, you don't really specify the problem very well: saying "antechber
on po4 dose not generate divcon files" is vague; an exact error message would
be much more helpful. You may also need to update to the current version of
AmberTools, since most versions of antechamber do not use divcon at all.

Fourth, you should check to be sure that your phosphate group has a full -3
charge, which is unusual. Remember that protons are generally missing from
X-ray structures.

...dac

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