AMBER Archive (2008)

Subject: Re: AMBER: Hybrid REMD amber10

From: Geoff Wood (geoffrey.wood_at_epfl.ch)
Date: Tue May 20 2008 - 09:24:11 CDT

Ok, thanks for the advice.

----------------------------------------------------------------------------------------------------------------------------------
Dr Geoffrey Wood
Ecole Polytechnique Fédérale de Lausanne http://lcbcpc21.epfl.ch/Group_members/geoff/
SB - ISIC - LCBC
BCH
4108
                                                                       
tel: +41 21 693 03 23
CH - 1015 Lausanne e-
mail: geoffrey.wood_at_epfl.ch
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On May 20, 2008, at 8:55 AM, Carlos Simmerling wrote:

> yes Ross is right- make sure even though you make an explicit solvent
> prmtop that you choose the radii that you want for the GB part in
> leap.
>
>
> On Mon, May 19, 2008 at 11:51 AM, Ross Walker
> <ross_at_rosswalker.co.uk> wrote:
>> Hi Geoff,
>>
>>
>>
>> Adrian or Carlos may be able to comment more definitively on this
>> but I
>> think this essentially means that the GB radii are required –
>> obviously to
>> do the hybrid part of the REMD – even though this is a solvated
>> prmtop file.
>> This should always be true since I believe leap always writes the
>> radii to
>> the prmtop file even if you solvated it. (%FLAG RADII)
>>
>>
>>
>> The key point though I think is that you need to consider what GB
>> model you
>> will use as part of the REMD when creating the prmtop file. I.e. if
>> you plan
>> to use GB=1 or 7 then you are fine with the defaults but if you
>> want to use
>> GB=2 or 5 then you need to execute 'set default PBradii mbondi2' in
>> leap
>> before saving the prmtop file.
>>
>>
>>
>> All the best
>>
>> Ross
>>
>>
>>
>>
>>
>> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On
>> Behalf Of
>> Geoff Wood
>> Sent: Monday, May 19, 2008 5:42 AM
>> To: amber_at_scripps.edu
>> Subject: AMBER: Hybrid REMD amber10
>>
>>
>>
>> Dear Amber users,
>>
>>
>>
>> In amber10 the hybrid remd calculations have become a lot more
>> user-friendly, which is great. However, in the manual it states "In
>> particular this means that
>>
>> the correct GB radii must be specified in the fully solvated
>> topology file,"
>> I was wondering if anyone could elaborate on this?
>>
>>
>>
>> Thanks in advance.
>>
>>
>>
>> ----------------------------------------------------------------------------------------------------------------------------------
>>
>> Dr Geoffrey Wood
>>
>> Ecole Polytechnique Fédérale de Lausanne
>> http://lcbcpc21.epfl.ch/Group_members/geoff/
>>
>> SB - ISIC - LCBC
>>
>> BCH 4108
>> tel: +41 21 693 03 23
>>
>> CH - 1015 Lausanne
>> e-mail: geoffrey.wood_at_epfl.ch
>>
>> ----------------------------------------------------------------------------------------------------------------------------------
>>
>>
>
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail: carlos.simmerling_at_gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================
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