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From: Jason Swails <jason.swails.gmail.com>

Date: Wed, 11 Aug 2010 08:46:42 -0400

On Wed, Aug 11, 2010 at 5:55 AM, Catein Catherine <askamber23.hotmail.com>wrote:

*>
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*> Dear All,
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*>
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*>
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*>
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*> I would like to calculate a PMF for a reaction coordinates which involve
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*> forming bond between A-B, at the same time cleaving a bond between B-C.
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*>
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*>
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*>
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*> I learnt from Bud that I may use "generalized distance coordinate
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*> restraint" to set the restraint and define the reaction coordinates. I
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*> lookup the manual. I found the restaint is defined as
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*>
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*>
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*>
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*> U = k(w1|r1-r2|+w2|r3-r4|+w3|r5-r6|+w4|r7-r8|-r0)2
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*>
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*>
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*>
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*> Is it same as the restrainst defined for LCOD?
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*>
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*>
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*>
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*> I also want to reconfirm with you that if I should define the restraint
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*> files as follows, if I want to study the PMF when LCOD change from 1A to
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*> 10A?
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*>
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*>
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*> # reaction coordinates
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*> &rst iat(6)=A,B,B,C, r1=0., r2=1., r3=1., r4=10., rk2 = 30., rk3 = 30., /
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*>
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This should be iat, not iat(6). You also need numbers here, not letters,

but I assume you knew that. If you want a generalized distance restraint,

you also need to define the restraint weights (rstwt). Then that will be a

generalized distance restraint for the 2 distances. The restraint weights

are the w1, w2, ..., etc. in the formula you posted above.

Good luck!

Jason

*>
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*> Best regards,
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*>
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*> Catherine
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*>
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*>
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*>
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*>
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*> _______________________________________________
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*> AMBER mailing list
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*> AMBER.ambermd.org
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*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

Date: Wed, 11 Aug 2010 08:46:42 -0400

On Wed, Aug 11, 2010 at 5:55 AM, Catein Catherine <askamber23.hotmail.com>wrote:

This should be iat, not iat(6). You also need numbers here, not letters,

but I assume you knew that. If you want a generalized distance restraint,

you also need to define the restraint weights (rstwt). Then that will be a

generalized distance restraint for the 2 distances. The restraint weights

are the w1, w2, ..., etc. in the formula you posted above.

Good luck!

Jason

-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Aug 11 2010 - 06:00:06 PDT

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