Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats

[Anirban Ghosh]

Thanks Angel and Justin.
Will try out the options!

Regards,

-Anirban

On Tue, May 1, 2012 at 5:46 PM, Justin A. Lemkul  wrote:

>
>
> On 5/1/12 8:05 AM, Ángel Piñeiro wrote:
>
>> I guess there are better solutions but an alternative is to map your
>> bilayer to
>> MARTINI 
>> (http://md.chem.rug.nl/**cgmartini/)
>> and then to use SUGAR-PIE
>> (http://smmb.usc.es/sugarpie/**sugarpie.php)
>> to go to from MARTINI to all-atom
>> CHARMM36.
>>
>>
> Even simpler would be to fix the offending atom names and build a suitable
> .hdb entry (if one does not already exist) and produce the topology with
> pdb2gmx.  I would think it would then be far easier to preserve the
> original configurations of the lipids, rather than changing the resolution
> back and forth.
>
> -Justin
>
>  Hope it helps,
>>
>> Ángel.
>>
>>
>> On Tue, 2012-05-01 at 17:25 +0530, Anirban Ghosh wrote:
>>
>>> Hi ALL,
>>>
>>>
>>> I have a equilibrated POPC bilayer (100 ns run) that I have run using
>>> GROMOS
>>> ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation
>>> using
>>> CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming
>>> conventions
>>> (N, P, C, O) between this two FFs as a result of which pdb2gmx gives
>>> error.
>>> Can these atom names (hydrogens can be ignored) of my equilibrated POPC
>>> bilayer be changed manually and then used with CHARMM36 FF? Thanks a lot
>>> in
>>> advance.
>>>
>>>
>>>
>>>
>>> Regards,
>>>
>>>
>>> Anirban
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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] POPC: ff53a6 and CHARMM36 formats

[Justin A. Lemkul]

On 5/1/12 8:05 AM, Ángel Piñeiro wrote:

I guess there are better solutions but an alternative is to map your bilayer to
MARTINI (http://md.chem.rug.nl/cgmartini/) and then to use SUGAR-PIE
(http://smmb.usc.es/sugarpie/sugarpie.php) to go to from MARTINI to all-atom
CHARMM36.



Even simpler would be to fix the offending atom names and build a suitable .hdb 
entry (if one does not already exist) and produce the topology with pdb2gmx.  I 
would think it would then be far easier to preserve the original configurations 
of the lipids, rather than changing the resolution back and forth.


-Justin


Hope it helps,

Ángel.


On Tue, 2012-05-01 at 17:25 +0530, Anirban Ghosh wrote:

Hi ALL,


I have a equilibrated POPC bilayer (100 ns run) that I have run using GROMOS
ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation using
CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming conventions
(N, P, C, O) between this two FFs as a result of which pdb2gmx gives error.
Can these atom names (hydrogens can be ignored) of my equilibrated POPC
bilayer be changed manually and then used with CHARMM36 FF? Thanks a lot in
advance.




Regards,


Anirban
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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] POPC: ff53a6 and CHARMM36 formats

[Ángel Piñeiro]

I guess there are better solutions but an alternative is to map your
bilayer to MARTINI (http://md.chem.rug.nl/cgmartini/) and then to use
SUGAR-PIE (http://smmb.usc.es/sugarpie/sugarpie.php) to go to from
MARTINI to all-atom CHARMM36.

Hope it helps,

Ángel.


On Tue, 2012-05-01 at 17:25 +0530, Anirban Ghosh wrote:

> Hi ALL,
> 
> 
> 
> I have a equilibrated POPC bilayer (100 ns run) that I have run using
> GROMOS ff53a6 FF. Now, I wish to use this POPC bilayer for a new
> simulation using CHARMM36 FF in GROAMCS 4.5.5. There are differences
> in atom naming conventions (N, P, C, O) between this two FFs as a
> result of which pdb2gmx gives error. Can these atom names (hydrogens
> can be ignored) of my equilibrated POPC bilayer be changed manually
> and then used with CHARMM36 FF? Thanks a lot in advance.
> 
> 
> 
> 
> Regards,
> 
> 
> Anirban
> 
> -- 
> 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!
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[gmx-users] POPC: ff53a6 and CHARMM36 formats

[Anirban Ghosh]

Hi ALL,

I have a equilibrated POPC bilayer (100 ns run) that I have run using
GROMOS ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation
using CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming
conventions (N, P, C, O) between this two FFs as a result of which pdb2gmx
gives error. Can these atom names (hydrogens can be ignored) of my
equilibrated POPC bilayer be changed manually and then used with CHARMM36
FF? Thanks a lot in advance.


Regards,

Anirban
-- 
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