Re: [gmx-users] Fe atom problems....in simulation

[Justin A. Lemkul]

Kamalesh Roy wrote:

Can you send me the parameters I need to usefor FE



Most of the force fields in Gromacs have support for Fe built in, at least in 
the context of heme.  What is it that you're trying to do?  If you need new 
parameters for whatever reason, it will be very tricky to do so for a transition 
metal like Fe.  Consider the following:


http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species

-Justin



On Mon, Apr 16, 2012 at 2:55 PM, francesco oteri 
mailto:francesco.ot...@gmail.com>> wrote:


Hi,
You have to had LJ parameters in ffnonbonded.itp file in the
subfolder relative to your force-field

Francesco

Il giorno 16 aprile 2012 11:08, Kamalesh Roy
mailto:roy.kamales...@gmail.com>> ha scritto:

CAn any one siggest me how can I run simulation a protein
containing Fe atom,
I have changed the iions.itpfile and included there Fe in
residue type.dat
bu still it is returning an error.

FE parameter not found.

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-- 
Cordiali saluti, Dr.Oteri Francesco


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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] Fe atom problems....in simulation

[Kamalesh Roy]

Can you send me the parameters I need to usefor FE


On Mon, Apr 16, 2012 at 2:55 PM, francesco oteri
wrote:

> Hi,
> You have to had LJ parameters in ffnonbonded.itp file in the subfolder
> relative to your force-field
>
> Francesco
>
> Il giorno 16 aprile 2012 11:08, Kamalesh Roy ha 
> scritto:
>
>> CAn any one siggest me how can I run simulation a protein containing Fe
>> atom,
>> I have changed the iions.itpfile and included there Fe in residue
>> type.dat
>> bu still it is returning an error.
>>
>> FE parameter not found.
>>
>> --
>> 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
>>
>
>
>
> --
> Cordiali saluti, Dr.Oteri Francesco
>
> --
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Re: [gmx-users] Fe atom problems....in simulation

[francesco oteri]

Hi,
You have to had LJ parameters in ffnonbonded.itp file in the subfolder
relative to your force-field

Francesco

Il giorno 16 aprile 2012 11:08, Kamalesh Roy  ha
scritto:

> CAn any one siggest me how can I run simulation a protein containing Fe
> atom,
> I have changed the iions.itpfile and included there Fe in residue type.dat
> bu still it is returning an error.
>
> FE parameter not found.
>
> --
> 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
>



-- 
Cordiali saluti, Dr.Oteri Francesco
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