[AMBER] mol2 - pdb conversion

From: Taufik Al-Sarraj <taufik.alsarraj.utoronto.ca>
Date: Mon, 16 Mar 2009 21:38:09 +0000

Hi,

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.



Received on Wed Mar 18 2009 - 01:12:05 PDT
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