Re: [gmx-users] decimal charge instead of integer

[Chandan Choudhury]

Hi Tom !!!

Can you guide to incorporate the AMBER parameter for ATP (
http://www.pharmacy.manchester.ac.uk/bryce/amber#cof) in ffamber. I am using
ffamber for the simulation of Protein + ATP.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Thu, Jan 21, 2010 at 7:06 PM, Thomas Piggot wrote:

> If using an amber forcefield and GTP/GDP you can use the parameters on the
> following website. I have used the ATP/ADP ones and have had no problems
> with many different systems and ATP/ADP conformations with which I used to
> test these parameters.
>
> http://www.pharmacy.manchester.ac.uk/bryce/amber#cof
>
> Tom
>
>
> Justin A. Lemkul wrote:
>
>>
>>
>> Carla Jamous wrote:
>>
>>> Thank you Justin,
>>> but I ran a simulation before this one with GTP & it worked fine. GDP &
>>> GTP parameters are identical except for GDP having less atoms.
>>> This is why I can't understand why I don't get an integer charge while I
>>> did in my previous simulation.
>>>
>>>
>> OK, but this still doesn't help anyone give you any advice.  Please refer
>> to my previous post - which case applies to you: almost integer, or way off?
>>
>> It is also potentially faulty logic to suggest that GDP parameters can be
>> generated from GTP parameters by simply chopping off a phosphate.  Under
>> most force field parameter sets, the charges on the beta-phosphate will have
>> to change since the electronic properties of the molecule are now different.
>>
>> -Justin
>>
>>  Carla
>>>
>>> On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote:
>>>
>>>
>>>
>>>Carla Jamous wrote:
>>>
>>>Hi,
>>>
>>>In order to run my simulation, I had to insert GDP parameters in
>>>ffamber94 (the force field I'm using).
>>>However, I'm having a problem with GDP charge.
>>>the charge of every charge group in top file should be an
>>>integer. But I'm getting a decimal charge which gives me
>>>naturally a decimal total charge of my molecule.
>>>I checked number of atoms, it's correct, their charge also.
>>>But it seems it's having trouble adding charges & giving an
>>>integer charge.
>>>Does anyone have an idea where is the source of the problem?
>>>
>>>
>>>What is the charge?  If it is a small difference between an integer
>>>and your charge (i.e., the difference between +1. and +2) then
>>>there is no problem. The issue there is the inherent limitation of
>>>doing a lot of floating-point operations to sum the total charge.
>>> If, however, you have a charge of +1.9256 when you wanted +2, then
>>>your parameters are simply wrong.
>>>
>>>-Justin
>>>
>>>Thanks
>>>
>>>Carla
>>>
>>>
>>>-- 
>>>
>>>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/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/mailing_lists/users.php
>>>
>>>
>>>
>>
> --
> Thomas Piggot
> University of Bristol, UK.
>
> --
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Re: [gmx-users] decimal charge instead of integer

[Carla Jamous]

Thanks everyone,
you were right, it doesn't work if I only take off one phosphate from GTP. I
was using the wrong parameters, now I have an integer total charge.

Carla

On Thu, Jan 21, 2010 at 2:36 PM, Thomas Piggot wrote:

> If using an amber forcefield and GTP/GDP you can use the parameters on the
> following website. I have used the ATP/ADP ones and have had no problems
> with many different systems and ATP/ADP conformations with which I used to
> test these parameters.
>
> http://www.pharmacy.manchester.ac.uk/bryce/amber#cof
>
> Tom
>
>
> Justin A. Lemkul wrote:
>
>>
>>
>> Carla Jamous wrote:
>>
>>> Thank you Justin,
>>> but I ran a simulation before this one with GTP & it worked fine. GDP &
>>> GTP parameters are identical except for GDP having less atoms.
>>> This is why I can't understand why I don't get an integer charge while I
>>> did in my previous simulation.
>>>
>>>
>> OK, but this still doesn't help anyone give you any advice.  Please refer
>> to my previous post - which case applies to you: almost integer, or way off?
>>
>> It is also potentially faulty logic to suggest that GDP parameters can be
>> generated from GTP parameters by simply chopping off a phosphate.  Under
>> most force field parameter sets, the charges on the beta-phosphate will have
>> to change since the electronic properties of the molecule are now different.
>>
>> -Justin
>>
>>  Carla
>>>
>>> On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote:
>>>
>>>
>>>
>>>Carla Jamous wrote:
>>>
>>>Hi,
>>>
>>>In order to run my simulation, I had to insert GDP parameters in
>>>ffamber94 (the force field I'm using).
>>>However, I'm having a problem with GDP charge.
>>>the charge of every charge group in top file should be an
>>>integer. But I'm getting a decimal charge which gives me
>>>naturally a decimal total charge of my molecule.
>>>I checked number of atoms, it's correct, their charge also.
>>>But it seems it's having trouble adding charges & giving an
>>>integer charge.
>>>Does anyone have an idea where is the source of the problem?
>>>
>>>
>>>What is the charge?  If it is a small difference between an integer
>>>and your charge (i.e., the difference between +1. and +2) then
>>>there is no problem. The issue there is the inherent limitation of
>>>doing a lot of floating-point operations to sum the total charge.
>>> If, however, you have a charge of +1.9256 when you wanted +2, then
>>>your parameters are simply wrong.
>>>
>>>-Justin
>>>
>>>Thanks
>>>
>>>Carla
>>>
>>>
>>>-- 
>>>
>>>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/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/mailing_lists/users.php
>>>
>>>
>>>
>>
> --
> Thomas Piggot
> University of Bristol, UK.
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] decimal charge instead of integer

[Thomas Piggot]

If using an amber forcefield and GTP/GDP you can use the parameters on 
the following website. I have used the ATP/ADP ones and have had no 
problems with many different systems and ATP/ADP conformations with 
which I used to test these parameters.


http://www.pharmacy.manchester.ac.uk/bryce/amber#cof

Tom

Justin A. Lemkul wrote:



Carla Jamous wrote:

Thank you Justin,
but I ran a simulation before this one with GTP & it worked fine. GDP 
& GTP parameters are identical except for GDP having less atoms.
This is why I can't understand why I don't get an integer charge while 
I did in my previous simulation.




OK, but this still doesn't help anyone give you any advice.  Please 
refer to my previous post - which case applies to you: almost integer, 
or way off?


It is also potentially faulty logic to suggest that GDP parameters can 
be generated from GTP parameters by simply chopping off a phosphate.  
Under most force field parameter sets, the charges on the beta-phosphate 
will have to change since the electronic properties of the molecule are 
now different.


-Justin


Carla

On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul > wrote:




Carla Jamous wrote:

Hi,

In order to run my simulation, I had to insert GDP parameters in
ffamber94 (the force field I'm using).
However, I'm having a problem with GDP charge.
the charge of every charge group in top file should be an
integer. But I'm getting a decimal charge which gives me
naturally a decimal total charge of my molecule.
I checked number of atoms, it's correct, their charge also.
But it seems it's having trouble adding charges & giving an
integer charge.
Does anyone have an idea where is the source of the problem?


What is the charge?  If it is a small difference between an integer
and your charge (i.e., the difference between +1. and +2) then
there is no problem. The issue there is the inherent limitation of
doing a lot of floating-point operations to sum the total charge.
 If, however, you have a charge of +1.9256 when you wanted +2, then
your parameters are simply wrong.

-Justin

Thanks

Carla


-- 

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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--
Thomas Piggot
University of Bristol, UK.
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Re: [gmx-users] decimal charge instead of integer

[Justin A. Lemkul]

Carla Jamous wrote:

Thank you Justin,
but I ran a simulation before this one with GTP & it worked fine. GDP & 
GTP parameters are identical except for GDP having less atoms.
This is why I can't understand why I don't get an integer charge while I 
did in my previous simulation.




OK, but this still doesn't help anyone give you any advice.  Please refer to my 
previous post - which case applies to you: almost integer, or way off?


It is also potentially faulty logic to suggest that GDP parameters can be 
generated from GTP parameters by simply chopping off a phosphate.  Under most 
force field parameter sets, the charges on the beta-phosphate will have to 
change since the electronic properties of the molecule are now different.


-Justin


Carla

On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul > wrote:




Carla Jamous wrote:

Hi,

In order to run my simulation, I had to insert GDP parameters in
ffamber94 (the force field I'm using).
However, I'm having a problem with GDP charge.
the charge of every charge group in top file should be an
integer. But I'm getting a decimal charge which gives me
naturally a decimal total charge of my molecule.
I checked number of atoms, it's correct, their charge also.
But it seems it's having trouble adding charges & giving an
integer charge.
Does anyone have an idea where is the source of the problem?


What is the charge?  If it is a small difference between an integer
and your charge (i.e., the difference between +1. and +2) then
there is no problem. The issue there is the inherent limitation of
doing a lot of floating-point operations to sum the total charge.
 If, however, you have a charge of +1.9256 when you wanted +2, then
your parameters are simply wrong.

-Justin

Thanks

Carla


-- 



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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--


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] decimal charge instead of integer

[Erik Marklund]

Carla Jamous skrev:

Thank you Justin,
but I ran a simulation before this one with GTP & it worked fine. GDP 
& GTP parameters are identical except for GDP having less atoms.
This is why I can't understand why I don't get an integer charge while 
I did in my previous simulation.


Carla

Well, if you removed one phosphate group you may not have removed 
exactly -1 e. What do the rtp-entries look like?


Erik
On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul > wrote:




Carla Jamous wrote:

Hi,

In order to run my simulation, I had to insert GDP parameters
in ffamber94 (the force field I'm using).
However, I'm having a problem with GDP charge.
the charge of every charge group in top file should be an
integer. But I'm getting a decimal charge which gives me
naturally a decimal total charge of my molecule.
I checked number of atoms, it's correct, their charge also.
But it seems it's having trouble adding charges & giving an
integer charge.
Does anyone have an idea where is the source of the problem?


What is the charge?  If it is a small difference between an
integer and your charge (i.e., the difference between +1. and
+2) then there is no problem. The issue there is the inherent
limitation of doing a lot of floating-point operations to sum the
total charge.  If, however, you have a charge of +1.9256 when you
wanted +2, then your parameters are simply wrong.

-Justin

Thanks

Carla


-- 



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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--
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys

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Re: [gmx-users] decimal charge instead of integer

[Erik Marklund]

Carla Jamous skrev:

Hi,

In order to run my simulation, I had to insert GDP parameters in 
ffamber94 (the force field I'm using).

However, I'm having a problem with GDP charge.
the charge of every charge group in top file should be an integer. But 
I'm getting a decimal charge which gives me naturally a decimal total 
charge of my molecule.

I checked number of atoms, it's correct, their charge also.
But it seems it's having trouble adding charges & giving an integer 
charge.

Does anyone have an idea where is the source of the problem?

Thanks

Carla
I don't think amber uses charge groups, so there is no need to put that 
constraint on your set of charges. The moleculs as a whole must have 
integer charge though.


--
---
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://xray.bmc.uu.se/molbiophys

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Re: [gmx-users] decimal charge instead of integer

[Carla Jamous]

Thank you Justin,
but I ran a simulation before this one with GTP & it worked fine. GDP & GTP
parameters are identical except for GDP having less atoms.
This is why I can't understand why I don't get an integer charge while I did
in my previous simulation.

Carla

On Thu, Jan 21, 2010 at 2:15 PM, Justin A. Lemkul  wrote:

>
>
> Carla Jamous wrote:
>
>> Hi,
>>
>> In order to run my simulation, I had to insert GDP parameters in ffamber94
>> (the force field I'm using).
>> However, I'm having a problem with GDP charge.
>> the charge of every charge group in top file should be an integer. But I'm
>> getting a decimal charge which gives me naturally a decimal total charge of
>> my molecule.
>> I checked number of atoms, it's correct, their charge also.
>> But it seems it's having trouble adding charges & giving an integer
>> charge.
>> Does anyone have an idea where is the source of the problem?
>>
>>
> What is the charge?  If it is a small difference between an integer and
> your charge (i.e., the difference between +1. and +2) then there is no
> problem. The issue there is the inherent limitation of doing a lot of
> floating-point operations to sum the total charge.  If, however, you have a
> charge of +1.9256 when you wanted +2, then your parameters are simply wrong.
>
> -Justin
>
>  Thanks
>>
>> Carla
>>
>>
> --
> 
>
> 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
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Re: [gmx-users] decimal charge instead of integer

[David van der Spoel]

On 1/21/10 2:12 PM, Carla Jamous wrote:

Hi,

In order to run my simulation, I had to insert GDP parameters in
ffamber94 (the force field I'm using).
However, I'm having a problem with GDP charge.
the charge of every charge group in top file should be an integer. But
I'm getting a decimal charge which gives me naturally a decimal total
charge of my molecule.
I checked number of atoms, it's correct, their charge also.
But it seems it's having trouble adding charges & giving an integer charge.
Does anyone have an idea where is the source of the problem?


In your topology most likely. Maybe you are missing a H atom?

Thanks

Carla




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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Re: [gmx-users] decimal charge instead of integer

[Justin A. Lemkul]

Carla Jamous wrote:

Hi,

In order to run my simulation, I had to insert GDP parameters in 
ffamber94 (the force field I'm using).

However, I'm having a problem with GDP charge.
the charge of every charge group in top file should be an integer. But 
I'm getting a decimal charge which gives me naturally a decimal total 
charge of my molecule.

I checked number of atoms, it's correct, their charge also.
But it seems it's having trouble adding charges & giving an integer charge.
Does anyone have an idea where is the source of the problem?



What is the charge?  If it is a small difference between an integer and your 
charge (i.e., the difference between +1. and +2) then there is no problem. 
The issue there is the inherent limitation of doing a lot of floating-point 
operations to sum the total charge.  If, however, you have a charge of +1.9256 
when you wanted +2, then your parameters are simply wrong.


-Justin


Thanks

Carla



--


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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[gmx-users] decimal charge instead of integer

[Carla Jamous]

Hi,

In order to run my simulation, I had to insert GDP parameters in ffamber94
(the force field I'm using).
However, I'm having a problem with GDP charge.
the charge of every charge group in top file should be an integer. But I'm
getting a decimal charge which gives me naturally a decimal total charge of
my molecule.
I checked number of atoms, it's correct, their charge also.
But it seems it's having trouble adding charges & giving an integer charge.
Does anyone have an idea where is the source of the problem?

Thanks

Carla
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