Re: [AMBER] mol2 - pdb conversion

From: Taufik Al-Sarraj <>
Date: Wed, 18 Mar 2009 19:20:54 +0000

Hi David,
Thank you i will try and fix the number of digits for the atoms. How did
you find out the number of atoms that have no bonds? because i should
remove those H and O that are floating around.

David A. Case wrote:
> 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

AMBER mailing list
Received on Fri Mar 20 2009 - 01:10:34 PDT
Custom Search