[gmx-users] Arginine_Hydrochloride topology
Justin A. Lemkul
jalemkul at vt.edu
Fri Aug 12 14:08:58 CEST 2011
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.__au
> <mailto:Mark.Abraham at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> |
> (540) 231-9080
>
>
> http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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> --
> ==============================__==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> 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
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================__==========
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--
========================================
Justin A. Lemkul
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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