Re: [AMBER] mol2 - pdb conversion

From: David A. Case <>
Date: Tue, 17 Mar 2009 15:47:53 +0000

On Mon, Mar 16, 2009, Taufik Al-Sarraj wrote:
> I have a mol2 file and a frcmod file (attached) that i recently used to
> simulate a surface. the simulation runs so the prmtop file and inpcrd
> files are okay, however if i try and create a pdb file from the output
> files, ambpdb -p surf.prmtop <surf.res> surf.pdb the structure (bonds)
> and some of the atoms are incorrect. So i tried this
> xleap
> source leaprc.gaff
> loadamberparams mysioforce.frcmod
> surf = loadmol2 SiO2APTMS.mol2
> edit surf --it looks right
> saveamberparm surf surf.prmtop surf.inpcrd
> outside xleap
> ambpdb -p surf.prmtop <surf.inpcrd> surf.pdb
> the file surf.pdb is not the same as the original mol2 file, some Si
> atoms are labeled L and the bonds are all gone. i tried ambpdb -bres
> option, and the outcome is the same.
> it is important to create a pdb or a mol2 file of the (surf.prmtop
> surf.rst output) correctly, i am not sure how.

First, many of the atom names in your mol2 file have more than four
characters, but Amber (and PDB) atom names have a limit of four. You
will have to change the atom names. (Basically, all silcon atoms with a
number greater than 100, or hydrogens/oxygens with a number greater than 1000.)

Second, there appear to be a number of hydrogens in the system that have
no covalent bonds (e.g. H131, H271, etc.) I'm not sure if this is what
you want or not.

...good luck...dac

AMBER mailing list
Received on Wed Mar 18 2009 - 01:17:07 PDT
Custom Search