AMBER Archive (2008)

Subject: RE: AMBER: Hybrid REMD amber10

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon May 19 2008 - 10:51:13 CDT

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.

 

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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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