AMBER Archive (2009)

Subject: Re: [AMBER] mol2 - pdb conversion

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Mar 17 2009 - 10:47:53 CDT

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

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