shahid nayeem wrote:
I tried with single Arginine molecule pdb.
pdb2gmx -f arg.pdb -o arg.gro -p arg.top
genconf -f arg.gro -nbox 2 2 2 -o seq.gro
genbox -cp seq.gro -cs spc216.gro -ci protein.pdb -nmol 1 -o seq_box.gro
-box 1.8 1.8 1.8
command runs but it does not add protein.pdb to the box
What is in protein.pdb? I don't believe genbox can handle multi-residue
molecules, but I could be wrong. Or there could be insufficient space, which is
quite likely. A 1.8-nm box is too small for all but the tiniest proteins. The
better approach:
1. Run pdb2gmx on protein.pdb
2. Run pdb2gmx on arg.pdb, convert the .top to .itp and #include it in the .top
from (1)
3. Run genbox -ci to add arg.gro molecules into the system
-Justin
shahid nayeem
On Fri, Aug 12, 2011 at 4:32 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
shahid nayeem wrote:
I couldn't get you. Does it means that for pre-positioning say
40 molecules of Arginine do I need to create 40 pdb of different
coordinate then combine it with pdb of protein and then use
pdb2gmx. I want to use different number of free positively
charged Arginine molecule in simulation box along with protein.
shahid nayeem
Treat the system like you would any other "normal" protein. Run
pdb2gmx on a coordinate file of a single molecule and proceed with
building your system, which can include replication (i.e. genconf to
get multiple molecules), genbox (to add other molecules and
solvent), and genion. For systems with different numbers of
arginine, simply alter the corresponding line in the [molecules]
directive of the topology that pdb2gmx wrote.
-Justin
On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.__au
<mailto:mark.abra...@anu.edu.au>>> wrote:
On 11/08/2011 7:24 PM, shahid nayeem wrote:
Hi Justin
I prepared a box of SOL and arginine Hydrochloride. But
when I
solvate my protein with this box now the positively charged
arginine is as solvent and this causes problem in grompp.
It gives
error like "No such Molecule types ARG" etc. Solvating
arginine
with water and preparing a box was without error. which
forcefield
in gromacs has inbuilt .itp file for free amino acid
which I can
include in my .top file.
See
http://www.gromacs.org/__Documentation/How-tos/__Multiple_Chains
<http://www.gromacs.org/Documentation/How-tos/Multiple_Chains>.
Pre-position the non-water molecules, use pdb2gmx, solvate.
Mark
Shahid Nayeem
On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
shahid nayeem wrote:
Dear All I am trying to find the topology and
parameterof
free Arginine Hydrchloride molecule in gromacs
force-field
format. Developing it in Pro-Drg will not serve
as I will
need some other parametrization tool to check it
charges.
If someone can help, I will be grateful.
Isn't this just a protonated arginine (normal state for
neutral pH) with a chloride counterion? There's nothing
special about it, just run a coordinate file through
pdb2gmx
with the force field of your choice.
-Justin
-- ==============================__==========
Justin A. Lemkul
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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