Re: [gmx-users] Arginine_Hydrochloride topology

[Justin A. Lemkul]

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 > 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
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
.
   Pre-position the non-water molecules, use pdb2gmx, solvate.

   Mark


   Shahid Nayeem

   On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul
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
   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



   ==__==
   -- gmx-users mailing list  
 gmx-users@gromacs.org 

   >

   http://lists.gromacs.org/__mailman/listinfo/gmx-users

   Please search the archive at
   http://www.gromacs.org/__Support/Mailing_Lists/Search

Re: [gmx-users] Arginine_Hydrochloride topology

[shahid nayeem]

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  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 >> 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
>> .
>>Pre-position the non-water molecules, use pdb2gmx, solvate.
>>
>>Mark
>>
>>
>> Shahid Nayeem
>>>
>>>On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul >>> 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  | (540) 231-9080
>>>
>>>
>>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>>>
>>>==**==
>>>-- gmx-users mailing listgmx-users@gromacs.org
>>>
>>>
>>>
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>>>Please search the archive at
>>>
>>> http://www.gromacs.org/**Support/Mailing_Lists/Searchbefore
>>>posting!
>>>Please don't post (un)subscribe requests to the list. Use the
>>>www interface or send it to gmx-users-requ...@gromacs.org
>>>
>>> >> >.
>>>
>>>Can't post? Read 
>>> http://www.gromacs.org/**Support/Mailing_Lists
>>>
>>>
>>>
>>>
>>>
>>
>>--
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>>Please search the archive at
>>
>> http://www.gromacs.org/**Support/Mailing_Lists/Searchbefore
>>  posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-requ...@gromacs.org
>>> >.
>>
>>Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>>
>>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
>

Re: [gmx-users] Arginine_Hydrochloride topology

[Justin A. Lemkul]

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 > 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.
Pre-position the non-water molecules, use pdb2gmx, solvate.

Mark



Shahid Nayeem

On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul 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
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


-- 
gmx-users mailing listgmx-users@gromacs.org


http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists







--
gmx-users mailing listgmx-users@gromacs.org

http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists




--


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


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Arginine_Hydrochloride topology

[shahid nayeem]

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

On Thu, Aug 11, 2011 at 3:15 PM, Mark Abraham 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.
> Pre-position the non-water molecules, use pdb2gmx, solvate.
>
> Mark
>
>
>  Shahid Nayeem
>
> On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul  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 | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>>  --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Arginine_Hydrochloride topology

[Mark Abraham]

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. 
Pre-position the non-water molecules, use pdb2gmx, solvate.


Mark


Shahid Nayeem

On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul > 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  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


-- 
gmx-users mailing list gmx-users@gromacs.org


http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists






-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Arginine_Hydrochloride topology

[shahid nayeem]

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.
Shahid Nayeem

On Fri, Jul 29, 2011 at 5:02 PM, Justin A. Lemkul  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 | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Arginine_Hydrochloride topology

[Justin A. Lemkul]

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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists