Hi,
On Fri, Jun 28, 2013 at 11:28 AM, Hunter Brown
<bassoongoon.earthlink.net> wrote:
> The file '2LMP_3fold_postive_stagger_fibril.pdb' is the unmodified (except for the name) PDB file for 2LMP from RCSB.
This file is actually modified quite a bit from the original PDB, but
in mostly good ways (as far as LEaP is concerned); the extra models
have been removed, etc.. It is missing TER cards but it does have
chain IDs and LEaP is smart enough to start a new molecule when the
chain ID changes. When I load this PDB I only get 18 issues:
"Created a new atom named: H within residue: .R<NGLY 9>"
A quick look at the PDB shows that the first glycine of each chain
contains an atom named 'H', and if you look at the template for NGLY
in LEaP you'll see it expects the amine hydrogens to be named 'H1',
'H2', and 'H3'. The solution here is to strip all atoms named H from
residues named GLY (using something like cpptraj) and let LEaP build
the hydrogens back in, using this cpptraj input:
parm 2LMP_3fold_postive_stagger_fibril.pdb
trajin 2LMP_3fold_postive_stagger_fibril.pdb
strip :GLY.H
trajout 2LMP.stripGLYH.pdb
The resulting PDB can now be loaded into LEaP with no issues; all
missing hydrogens are built back in from templates. You can actually
do all of the PDB pre-processing with cpptraj using the original PDB
file you got from RSCB:
parm 2LMP.pdb
trajin 2LMP.pdb
strip :GLY.H
trajout 2LMP.stripGLYH.pdb onlyframes 1 # This indicates you only want
to write out MODEL 1
You can then solvate and add ions in LEaP. It's usually a good idea to
create your system in steps (in this case the non-solvated system),
both for error checking and because it can be useful later (if you
want to analyze a stripped trajectory for example).
> '3foldposionized.pdb' is the solvated and ionized PDB file I created with VMD.
>
> '3foldposionizedamber.pdb' is the solvated and ionized PDB file created by running '3foldposionized.pdb' through the charmm2amberlipid.x script.
There are a lot of issues with these PDBs. First of all the atom names
have changed (which is what lead to your previous error), and second
everything has the same chain ID and there are no TER cards, so as far
as LEaP is concerned everything should be in the same molecule which
is definitely not what you want. Unless you have a specific reason not
to, I would recommend using LEaP to build your entire molecule if you
are going to be performing simulations using Amber.
Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Jun 28 2013 - 13:00:02 PDT
