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 - 10:54:25 CDT

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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