AMBER Archive (2005)

Subject: Re: AMBER: Using OPLS atom types

From: Furse, Kristina Elisabet (kristina.e.furse_at_vanderbilt.edu)
Date: Tue Nov 22 2005 - 11:10:06 CST

Hi Lorna-

When I used OPLS atom types in amber8 for a hybrid all-atom/united-atom
simulation, I just grabbed the ones I needed and made a new frcmod file out of
them, and did the conversion for the vdw parameters by hand so I had control of
the whole operation. Maybe someone else has an easier way.

Kristina

Quoting Lorna Stimson <lorna.stimson_at_gmail.com>:

> Hi,
>
> I am trying to use OPLS atom type in amber, i have altered the
> opls_parm.dat file to the new format and removed the non-bonded STDU
> and STUB vdw parameters and everything seems OK, except that the "AC"
> flag which specifies c6-c12 style params instead of "RE" for radius,
> thus the vdw energy is ridiculous.
>
> Is there another flag to specify the format of the vdw parameters
> which must be set in leap?
>
> Does anyone have experience using other than the "RE" flag which may
> help me track down the problem?
>
> Below is the tail of my parm file.
>
> Thanks,
>
> Lorna
>
>
> C2-OS-P -O2 3 0.75 0. 3.
> From X -OS-P -X
> OS-C2-CH-OS 1 1.0 0. -3.
> OS-C2-CH-OS 1 0.5 0. 2.
> OS-P -OS-C2 1 .25 0. -3.
> OS-P -OS-C2 1 .75 0. 2.
> C2-C2-C -OS 2 0.0 180. 3.
> From X -C2-C -X
> C2-C2-C -O 2 0.0 180. 3.
> From X -C2-C -X
> CH-C2-OS-P 1 1.45 0. 3.
> From X -C2-OS-X
> C2-C2-OS-P 1 1.45 0. 3.
> From X -C2-OS-X
> CH-C2-OS-C 1 1.45 0. 3.
> From X -C2-OS-X
> O -C -OS-C2 1 2.25 180. -2.
> Gdansk, M.P.-G. 20.06.'97
> O -C -OS-C2 1 2.70 180. 1.
> Gdansk, M.P.-G. 20.06.'97
>
> OS-CH-C2-C2 3 14.0 180. 3.
> From X -CH-C2-X
>
>
>
> OPLS AC
> CH 2901000.0 963.5
> C3 8171500.0 2286.9
> C2 5934600.0 1673.7
> C 3248100.0 1168.0
> OS 361380.0 495.7
> O 380000.0 565.0
> O2 380000.0 565.0
> N3 944300.0 801.3
> P 7113043.3 2667.0
> HW 0.0 0.0 TIP3P water model
> OW 582000.0 595.0 TIP3P water model
> XE 23871780.0 6430.0 From opls.info
> xe 3.935 0.4330 => 6.430079e+03 2.387178e+07
>
> END
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-----------------------------------------------------------------
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Email: kristina.e.furse_at_Vanderbilt.Edu
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