AMBER Archive (2008)

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

From: Waqas Nasir (nasirwaqas1983_at_yahoo.com)
Date: Mon Sep 15 2008 - 10:47:00 CDT

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.
>
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Professor, Department of Chemistry
CMM Bldg, Room G80 Phone: (631) 632-1336 Fax: 632-1555
Stony Brook University E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
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