AMBER Archive (2008)

Subject: Re: AMBER: Hydrogen bond energies in explicit solvent.

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Sep 15 2008 - 11:24:07 CDT

they are not separable, but you could change the code to do so.

On Mon, Sep 15, 2008 at 12:17 PM, Waqas Nasir <nasirwaqas1983_at_yahoo.com> wrote:
> Is there anyway to separate out hbond energies from electrostatics.
>
> I will hopefully start the calculations again with ff99SB forcefield.
>
> Thanks,
> Waqas.
> ----- Original Message ----
> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
> To: amber_at_scripps.edu
> Sent: Monday, September 15, 2008 6:54:25 PM
> Subject: Re: AMBER: Hydrogen bond energies in explicit solvent.
>
> it is fine that ehbond is zero, the hbond energies are part of the
> electrostatics.
>
> not sure why you switched to ff03 after my discussion- I recommend ff99SB.
> amber8 is quite old, newer versions are much faster in addition to
> having more options.
>
> On Mon, Sep 15, 2008 at 11:47 AM, Waqas Nasir <nasirwaqas1983_at_yahoo.com>
> wrote:
>> Sorry for not making it clear, I meant the EHBOND field, that is zero
>> below
>> which is an excerpt from the mdout file.
>>
>> --------------------------------------------------------------------------
>> KE Trans = 0.8437 KE Rot = 0.4377 C.O.M. Vel = 0.004890
>>
>> Translational and rotational motion removed
>>
>> KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000
>>
>> NSTEP = 170000 TIME(PS) = 350.000 TEMP(K) = 299.49 PRESS =
>> 0.0
>> Etot = -3255.0722 EKtot = 7269.0626 EPtot =
>> -10524.1348
>> BOND = 1751.1156 ANGLE = 4460.6537 DIHED =
>> 2753.7859
>> 1-4 NB = 2308.0709 1-4 EEL = 24770.3355 VDWAALS =
>> -4834.8438
>> EELEC = -45350.4430 EHBOND = 0.0000 RESTRAINT =
>> 3617.1904
>> EAMBER (non-restraint) = -14141.3252
>>
>> ------------------------------------------------------------------------------
>>
>> I am using sugar/protein complexes, I just wanted to ask another small
>> question about the force field. I had switched to ff03 after your last
>> discussion a week ago. Now is that ok to stick with it or you think ff99SB
>> is a better choice given the system that I have. Because I have to do a
>> series of studies on different complexes.
>>
>> Moreover, will the results be different for ff03 in case of EHBOND? I am
>> asking you this because the sugars in this case have water mediated
>> interactions and they are there to play a vital role in binding studies.
>>
>> Thanks alot,
>> Waqas.
>>
>>
>> ----- Original Message ----
>> From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
>> To: amber_at_scripps.edu
>> Sent: Monday, September 15, 2008 6:01:41 PM
>> Subject: Re: AMBER: Hydrogen bond energies in explicit solvent.
>>
>> please note that the amber developers recommend that you do NOT use
>> ff99. many studies have shown that this is not a good model. please
>> use ff99SB or ff03 (ff99SB is newest).
>>
>> what do you mean by the "HB field"? there are no explicit hydrogen
>> bonding terms needed, it will be handled by the electrostatics. the
>> same is true for ff99, ff03 and ff99SB.
>>
>> On Mon, Sep 15, 2008 at 10:56 AM, Waqas Nasir <nasirwaqas1983_at_yahoo.com>
>> wrote:
>>> Hi,
>>>
>>> Hope every thing is working fine at your side.
>>>
>>> Just wanted to ask about the HB field for the mdrun with explicit
>>> solvent.
>>> I
>>> have this field zero for the explicit solvent with solventcap option
>>> used.
>>> Is this because of the ff99 force field or is it due to something else?
>>> Is
>>> there a way to calculate the energy for HB? Moreover, will this not be
>>> the
>>> case with ff03 forcefield.
>>>
>>> Appreciate your comments,
>>> Thanks,
>>> Waqas.
>>>
>>> PS: I am using amber version 8.0 with ff99 and glycam06 forcefields.
>>>
>>>
>>
>>
>>
>> --
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-- 
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Carlos L. Simmerling, Ph.D.
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