Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

[Smith, Micholas D.]

Matthew,

Quick question, what are you trying to examine with the addition of bicarbonate?

-Micholas

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 on behalf of Faulkner, 
Matthew 
Sent: Friday, September 04, 2015 7:42 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Force field selection for free Bicarbonate molecules in
solution

I am trying to find a suitable force field for using Bicarbonate in an aqueous 
environment in my MDS. I can't find anything where Bicarbonate has been used 
this way in gromacs in the literature, does anybody know of a reference for me 
or have advice on which force filed would be best?

I have run several MDS in the OPLS-AA force field for my protein of interest in 
solution with water and various ions and they work very well,but I would like 
to add 150 mM HCO3- into my environment. I have a PDB and TOP file prepared 
using PRODRG for the HCO3- but I'm not sure if the OPLS-AA force field is 
suitable for this molecule.

Regards,
Matthew.
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Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

[Justin Lemkul]

On 9/4/15 9:07 AM, Faulkner, Matthew wrote:

Thank you Justin,

Do you know a suitable force field to use for a topolgy from PRODRG? I am aware 
that the topology from PRODRG may now be of the best quality but I want to run 
a short MDS as proof of concept first to see if the events I am interested in 
occur in a  reasonable timeframe.



GROMOS.  Be sure to fix the charges that PRODRG gives you, otherwise any 
simulation you run will have lots of artificial behavior.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

[Justin Lemkul]

On 9/4/15 7:42 AM, Faulkner, Matthew wrote:

I am trying to find a suitable force field for using Bicarbonate in an
aqueous environment in my MDS. I can't find anything where Bicarbonate has
been used this way in gromacs in the literature, does anybody know of a
reference for me or have advice on which force filed would be best?

I have run several MDS in the OPLS-AA force field for my protein of interest
in solution with water and various ions and they work very well,but I would
like to add 150 mM HCO3- into my environment. I have a PDB and TOP file
prepared using PRODRG for the HCO3- but I'm not sure if the OPLS-AA force
field is suitable for this molecule.



FWIW, PRODRG topologies are (1) very poor quality and (2) not compatible with 
OPLS.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

[Faulkner, Matthew]

Thank you Justin,

I will check the charges. 

I appreciate the help.


Matthew.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: 04 September 2015 14:11
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Force field selection for free Bicarbonate molecules 
in solution

On 9/4/15 9:07 AM, Faulkner, Matthew wrote:
> Thank you Justin,
>
> Do you know a suitable force field to use for a topolgy from PRODRG? I am 
> aware that the topology from PRODRG may now be of the best quality but I want 
> to run a short MDS as proof of concept first to see if the events I am 
> interested in occur in a  reasonable timeframe.
>

GROMOS.  Be sure to fix the charges that PRODRG gives you, otherwise any
simulation you run will have lots of artificial behavior.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

[Faulkner, Matthew]

Micholas,

I have a protein which has a pore through the centre believed to act as channel 
for a range of molecules, Bicarbonate is one of them. I want to see if 
Bicarbonate passes through the channel and what happens as it does. I already 
have interesting events like this for ions I can add using genion so I want to 
run the same MDS with Bicarbonate. 

Matthew.

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Smith, 
Micholas D. [smit...@ornl.gov]
Sent: 04 September 2015 13:26
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Force field selection for free Bicarbonate molecules 
insolution

Matthew,

Quick question, what are you trying to examine with the addition of bicarbonate?

-Micholas

===
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Faulkner, 
Matthew <m.faulk...@liverpool.ac.uk>
Sent: Friday, September 04, 2015 7:42 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Force field selection for free Bicarbonate molecules in
solution

I am trying to find a suitable force field for using Bicarbonate in an aqueous 
environment in my MDS. I can't find anything where Bicarbonate has been used 
this way in gromacs in the literature, does anybody know of a reference for me 
or have advice on which force filed would be best?

I have run several MDS in the OPLS-AA force field for my protein of interest in 
solution with water and various ions and they work very well,but I would like 
to add 150 mM HCO3- into my environment. I have a PDB and TOP file prepared 
using PRODRG for the HCO3- but I'm not sure if the OPLS-AA force field is 
suitable for this molecule.

Regards,
Matthew.
--
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Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

[Faulkner, Matthew]

Thank you Justin,

Do you know a suitable force field to use for a topolgy from PRODRG? I am aware 
that the topology from PRODRG may now be of the best quality but I want to run 
a short MDS as proof of concept first to see if the events I am interested in 
occur in a  reasonable timeframe.

Regards,
Matthew.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul 
[jalem...@vt.edu]
Sent: 04 September 2015 13:58
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Force field selection for free Bicarbonate molecules 
in solution

On 9/4/15 7:42 AM, Faulkner, Matthew wrote:
> I am trying to find a suitable force field for using Bicarbonate in an
> aqueous environment in my MDS. I can't find anything where Bicarbonate has
> been used this way in gromacs in the literature, does anybody know of a
> reference for me or have advice on which force filed would be best?
>
> I have run several MDS in the OPLS-AA force field for my protein of interest
> in solution with water and various ions and they work very well,but I would
> like to add 150 mM HCO3- into my environment. I have a PDB and TOP file
> prepared using PRODRG for the HCO3- but I'm not sure if the OPLS-AA force
> field is suitable for this molecule.
>

FWIW, PRODRG topologies are (1) very poor quality and (2) not compatible with 
OPLS.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

[Vitaly V. Chaban]

My group works with the bicarbonate and similar anions in the context
of CO2 chemisorption.

You must exercise serious caution to assign correct electrostatic
potential at the surface of the anion and account for
hydration/solvation effects within the force field derivation
procedure.




On Fri, Sep 4, 2015 at 8:42 AM, Faulkner, Matthew
 wrote:
> I am trying to find a suitable force field for using Bicarbonate in an 
> aqueous environment in my MDS. I can't find anything where Bicarbonate has 
> been used this way in gromacs in the literature, does anybody know of a 
> reference for me or have advice on which force filed would be best?
>
> I have run several MDS in the OPLS-AA force field for my protein of interest 
> in solution with water and various ions and they work very well,but I would 
> like to add 150 mM HCO3- into my environment. I have a PDB and TOP file 
> prepared using PRODRG for the HCO3- but I'm not sure if the OPLS-AA force 
> field is suitable for this molecule.
>
> Regards,
> Matthew.
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> mail to gmx-users-requ...@gromacs.org.
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