[gmx-users] GMX to remove clashes?

[Liu, Liang]

Hi, all,
I am wondering if Gromacs can do the following work?

Assuming I have a pdb file of an RNA molecule. Some atoms may be too close
or even overlap, I am wondering if Gromacs can move the atoms to reasonable
positions and remove the bad contacts? The final structure is supposed to
be the "most" stable structure with minimal energy. I know AMBER
minimization can do this work, and I am wondering if Gromacs can do the
same?

-- 
Best,
Liang Liu
-- 
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Re: [gmx-users] GMX to remove clashes?

[Justin A. Lemkul]

Liu, Liang wrote:

Hi, all,
I am wondering if Gromacs can do the following work?

Assuming I have a pdb file of an RNA molecule. Some atoms may be too 
close or even overlap, I am wondering if Gromacs can move the atoms to 
reasonable positions and remove the bad contacts? The final structure is 
supposed to be the "most" stable structure with minimal energy. I know 
AMBER minimization can do this work, and I am wondering if Gromacs can 
do the same?




Gromacs is perfectly capable of energy minimization.  Whether or not 
minimization succeeds and gives a reasonable output is mostly dependent upon the 
feasibility of the starting structure.  If the minimization crashes, it's not 
Gromacs' fault ;)


-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


--
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Re: [gmx-users] GMX to remove clashes?

[Liu, Liang]

This is a "reasonable" answer :)

Thanks for that, and I just tried Gromacs for minimization, and looks the
final structure does not have clashes anymore, and also are very close to
the initial structure.

Another question is if there is a way to add ions automatically, meaning no
need to check the "NOTE" of "System has non-zero total charge" in the
output of grompp command? And also update the topology file automatically
too?

On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul  wrote:

>
>
> Liu, Liang wrote:
>
>> Hi, all,
>> I am wondering if Gromacs can do the following work?
>>
>> Assuming I have a pdb file of an RNA molecule. Some atoms may be too
>> close or even overlap, I am wondering if Gromacs can move the atoms to
>> reasonable positions and remove the bad contacts? The final structure is
>> supposed to be the "most" stable structure with minimal energy. I know
>> AMBER minimization can do this work, and I am wondering if Gromacs can do
>> the same?
>>
>>
> Gromacs is perfectly capable of energy minimization.  Whether or not
> minimization succeeds and gives a reasonable output is mostly dependent
> upon the feasibility of the starting structure.  If the minimization
> crashes, it's not Gromacs' fault ;)
>
> -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
>



-- 
Best,
Liang Liu
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] GMX to remove clashes?

[Justin A. Lemkul]

Liu, Liang wrote:

This is a "reasonable" answer :)

Thanks for that, and I just tried Gromacs for minimization, and looks 
the final structure does not have clashes anymore, and also are very 
close to the initial structure.


Another question is if there is a way to add ions automatically, meaning 
no need to check the "NOTE" of "System has non-zero total charge" in the 
output of grompp command? And also update the topology file 
automatically too?




That depends on the system.  For a simple solute in water, the running total 
charge of the solute is recorded in the qtot column of the .top file.  If you 
have a complex system with lots of charged things, no, there is no convenient 
way to get the charge aside from calculating it by hand or reading the grompp 
output.


The topology can be modified automatically by genion after ions are added by 
using the -p flag.


-Justin

On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul > wrote:




Liu, Liang wrote:

Hi, all,
I am wondering if Gromacs can do the following work?

Assuming I have a pdb file of an RNA molecule. Some atoms may be
too close or even overlap, I am wondering if Gromacs can move
the atoms to reasonable positions and remove the bad contacts?
The final structure is supposed to be the "most" stable
structure with minimal energy. I know AMBER minimization can do
this work, and I am wondering if Gromacs can do the same?


Gromacs is perfectly capable of energy minimization.  Whether or not
minimization succeeds and gives a reasonable output is mostly
dependent upon the feasibility of the starting structure.  If the
minimization crashes, it's not Gromacs' fault ;)

-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


==__==
-- 
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--
Best,
Liang Liu


--


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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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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Re: [gmx-users] GMX to remove clashes?

[Liu, Liang]

Thanks.

Do you know how to use a new force field, not amber or charm, but a force
field built by someone else, and it's already in Gromacs format (tons of
xvg file, right?)

On Mon, Nov 14, 2011 at 4:13 PM, Justin A. Lemkul  wrote:

>
>
> Liu, Liang wrote:
>
>> This is a "reasonable" answer :)
>>
>> Thanks for that, and I just tried Gromacs for minimization, and looks the
>> final structure does not have clashes anymore, and also are very close to
>> the initial structure.
>>
>> Another question is if there is a way to add ions automatically, meaning
>> no need to check the "NOTE" of "System has non-zero total charge" in the
>> output of grompp command? And also update the topology file automatically
>> too?
>>
>>
> That depends on the system.  For a simple solute in water, the running
> total charge of the solute is recorded in the qtot column of the .top file.
>  If you have a complex system with lots of charged things, no, there is no
> convenient way to get the charge aside from calculating it by hand or
> reading the grompp output.
>
> The topology can be modified automatically by genion after ions are added
> by using the -p flag.
>
> -Justin
>
>  On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Liu, Liang wrote:
>>
>>Hi, all,
>>I am wondering if Gromacs can do the following work?
>>
>>Assuming I have a pdb file of an RNA molecule. Some atoms may be
>>too close or even overlap, I am wondering if Gromacs can move
>>the atoms to reasonable positions and remove the bad contacts?
>>The final structure is supposed to be the "most" stable
>>structure with minimal energy. I know AMBER minimization can do
>>this work, and I am wondering if Gromacs can do the same?
>>
>>
>>Gromacs is perfectly capable of energy minimization.  Whether or not
>>minimization succeeds and gives a reasonable output is mostly
>>dependent upon the feasibility of the starting structure.  If the
>>minimization crashes, it's not Gromacs' fault ;)
>>
>>-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
>>
>>
>> 
>> >
>>
>>
>>
>>
>> --
>> Best,
>> Liang Liu
>>
>
> --
> ==**==
>
> 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
>



-- 
Best,
Liang Liu
-- 
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!
Plea

Re: [gmx-users] GMX to remove clashes?

[Justin A. Lemkul]

Liu, Liang wrote:

Thanks.

Do you know how to use a new force field, not amber or charm, but a 
force field built by someone else, and it's already in Gromacs format 
(tons of xvg file, right?)




Force fields are not in .xvg format, unless you're talking about using tabulated 
potentials.  In either case, please see the manual and the help information on 
gromacs.org, and start a new thread with more information to change topics if 
you have further questions.


-Justin

On Mon, Nov 14, 2011 at 4:13 PM, Justin A. Lemkul > wrote:




Liu, Liang wrote:

This is a "reasonable" answer :)

Thanks for that, and I just tried Gromacs for minimization, and
looks the final structure does not have clashes anymore, and
also are very close to the initial structure.

Another question is if there is a way to add ions automatically,
meaning no need to check the "NOTE" of "System has non-zero
total charge" in the output of grompp command? And also update
the topology file automatically too?


That depends on the system.  For a simple solute in water, the
running total charge of the solute is recorded in the qtot column of
the .top file.  If you have a complex system with lots of charged
things, no, there is no convenient way to get the charge aside from
calculating it by hand or reading the grompp output.

The topology can be modified automatically by genion after ions are
added by using the -p flag.

-Justin

On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:



   Liu, Liang wrote:

   Hi, all,
   I am wondering if Gromacs can do the following work?

   Assuming I have a pdb file of an RNA molecule. Some atoms
may be
   too close or even overlap, I am wondering if Gromacs can move
   the atoms to reasonable positions and remove the bad
contacts?
   The final structure is supposed to be the "most" stable
   structure with minimal energy. I know AMBER minimization
can do
   this work, and I am wondering if Gromacs can do the same?


   Gromacs is perfectly capable of energy minimization.  Whether
or not
   minimization succeeds and gives a reasonable output is mostly
   dependent upon the feasibility of the starting structure.  If the
   minimization crashes, it's not Gromacs' fault ;)

   -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


   >




-- 
Best,

Liang Liu


-- 
==__==


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.e