Re: [AMBER] status of the Amber lipid framework?

From: Jio M <jiomm.yahoo.com>
Date: Fri, 31 Jan 2014 06:00:24 -0800 (PST)

Dear Ross,


Glad (:
lipid 14 is available. I saw in paper it specifically says bugfix 21 needs to be applied for GPU. Can I check somehow whether it has been applied on our central cluster GPU facility?

Also can you please share mdin input files? I remember Callum once shared mdin files for GaffLipid. It will be of immense help.

Thanks

Jiom




On Thursday, January 30, 2014 7:28 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
 
Hi Igor,

The AMBER Lipid14 paper was published today. :-)
http://pubs.acs.org/doi/abs/10.1021/ct4010307

I've also put together a tar file of the Lipid14 (the new name) force
field which one can obtain here:
https://dl.dropboxusercontent.com/u/708185/lipid14_force_field_params_2014-
01-30.tar.gz

This should be placed in your AMBER 12 directory and untarred from there.
This way the paths will be correct and the various files will be placed in
the correct locations in the AMBER12 tree. You can load this in leap with
'source leaprc.lipid14'

Comments are welcome.

Official support for Lipid14 (as well additional barostats and other
tweaks for lipids) will be part of the upcoming AMBER14 release.

All the best
Ross


On 1/24/14, 9:12 AM, "Igor Marques" <igor.dragon88.gmail.com> wrote:

>dear ross,
>
>i understand that the lipid14 paper should still be under review, but,
>given your previous offer back in lausanne (october 2012), is it possible
>to send the forcefield files, for us to run some tests?
>
>many thanks,
>igor
>
>
>
> Igor Marques, PhD Student
>MSc in Pharmaceutical Biomedicine
>BSc in Biomedical Sciences
>
>Molecular Modeling Group University of
>Aveirohttp://molecular-modeling.dq.ua.pt/
>
>Mobile phone: +351 918 567 294
>Landline: +351 234 247 254
>Through PBX: +351 234 370 200 (ext. 22160)
>
>Universidade de Aveiro
>Campus Universitario de Santiago
>Agra do Crasto Edificio 30
>3810-193 Aveiro - Portugal
>
>
>
>On Thu, Dec 19, 2013 at 8:01 PM, Ross Walker <ross.rosswalker.co.uk>
>wrote:
>
>> Hi Sally,
>>
>> The paper describing it is currently under going review. Once it is
>> accepted (hopefully soon) we will make the parameter set (now called
>> Lipid14) publicly available.
>>
>> All the best
>> Ross
>>
>>
>> On 12/19/13 11:54 AM, "Sally Pias" <sallypias.gmail.com> wrote:
>>
>> >Hi all,
>> >
>> >Does anyone have news regarding the status of the updated Amber lipid
>> >force field and framework? Specifically, I am anticipating a merger
>> >of Lipid11 and GAFFLipid.
>> >
>> >Thanks,
>> >Sally Pias
>> >--
>> >Assistant Professor of Chemistry
>> >New Mexico Tech
>> >
>> >_______________________________________________
>> >AMBER mailing list
>> >AMBER.ambermd.org
>> >http://lists.ambermd.org/mailman/listinfo/amber

>>
>>
>>
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Received on Fri Jan 31 2014 - 06:30:02 PST
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