[gmx-users] Arginine_Hydrochloride topology
shahid nayeem
msnayeem at gmail.com
Fri Aug 12 14:04:12 CEST 2011
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
shahid nayeem
On Fri, Aug 12, 2011 at 4:32 PM, Justin A. Lemkul <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 <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>> 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> | (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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>>
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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