Hi,
Thank you for the response. I think what makes me confused is the scmask keyword. In the first case,
scmask=':3.CB,HB,CG2,HG21,HG22,HG23,OG1,HG1' for GTG and
scmask=':3.CB,HB1,HB2,HB3' for GAG
my understanding is that the atoms including ':3.CB,HB,CG2,HG21,HG22,HG23,OG1,HG1' are decoupled with softcore method from the surroundings while the atoms including scmask=':3.CB,HB1,HB2,HB3' are coupled to the surroundings.
In the second case,
scmask=':3.HB,CG2,HG21,HG22,HG23,OG1,HG1' for GTG and
scmask=':3.HB1,HB2,HB3' for GAG
atoms including ':3.HB,CG2,HG21,HG22,HG23,OG1,HG1' are decoupled with softcore method from the surroundings while the atoms including scmask=':3.HB1,HB2,HB3' are coupled to the surroundings. If my understanding is correct, I would expect the same deltaG values from one transformation since the initial and final state are the same for both cases (CB is a common atom in GTG and GAG, I would think it doesn't matter if I exclude it from scmask).
Best,
Lishan
----- Original Message -----
From: <steinbrt.rci.rutgers.edu>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Thursday, May 05, 2011 6:33 PM
Subject: Re: [AMBER] question about scmask
> Hi,
>
> two things:
>
> a) Are you talking about deltaG values from one transformation? These will
> certainly be different. Only deltadeltaG values from a properly set up
> thermodynamic cycle will give interpretable results.
>
> b) If you do get very different ddG values, this indicates that your
> simulation is not converged. You don't give simulation details, so it's
> impossible to judge that.
>
> Kind Regards,
>
> Thomas
>
> On Thu, May 5, 2011 5:29 am, Lishan Yao wrote:
>> Dear Amber users,
>>
>> I set up a alchemy simulation for the GTG to GAG mutation in water
>> (with head and tail groups neutralized). Following the typical
>> procedure, I did electrostatics first and then vdw. In the vdw alchemy
>> process, I used softcore method. But I got very different dv/dl values
>> when I use
>>
>> scmask=':3.CB,HB,CG2,HG21,HG22,HG23,OG1,HG1' for GTG and
>> scmask=':3.CB,HB1,HB2,HB3' for GAG
>> or
>> scmask=':3.HB,CG2,HG21,HG22,HG23,OG1,HG1' for GTG and
>> scmask=':3.HB1,HB2,HB3' for GAG
>>
>> I can't figure out what is the problem. It seems to me they should give
>> same or at least similar results.
>>
>> Best,
>> Lishan
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>>
>
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Thu May 05 2011 - 18:00:02 PDT
