[gmx-users] OPLS force field parameters

Fri Dec 13 19:16:45 CET 2013

Thanks Justin.

I already added the description in the ffbonded.itp, but nothing is shown in the topol file. I am not sure to put atom names (e.g. C9  C10) or atom type (C   C)? However, I tried both and non of them worked. I don't know what I am doing wrong and I appreciate if you could help me resolve my issue.

Kind regards,
Ehsan

----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, December 12, 2013 3:02:22 PM
Subject: Re: [gmx-users] OPLS force field parameters

On Thu, Dec 12, 2013 at 12:45 PM, Ehsan Sadeghi <esa38 at sfu.ca> wrote:

> Hi gmx users,
>
> I try to use OPLS force field for my simulation. I added the following
> residue to the aminoacids.rtp, but when I generate the topol.top file it
> does not show the the bond stretching, angle bond, dihedrals.
>
>
> [ NAF ]
>    [ atoms ]
>      C1    opls_966   0.3846     1
>      C2    opls_966   0.3846     1
>      C3    opls_966   0.3846     1
>      C4    opls_966   0.3846     1
>      F17   opls_972  -0.1923     1
>      F18   opls_972  -0.1923     1
>      F19   opls_972  -0.1923     1
>      F20   opls_972  -0.1923     1
>      F21   opls_972  -0.1923     1
>      F22   opls_972  -0.1923     1
>      F23   opls_972  -0.1923     1
>      F24   opls_972  -0.1923     1
>      C5    opls_966   0.3846     1
>      C6    opls_966   0.3846     1
>      C7    opls_966   0.3846     1
>      C8    opls_966   0.3846     1
>      F25   opls_972  -0.1923     1
>      F26   opls_972  -0.1923     1
>      F27   opls_972  -0.1923     1
>      F28   opls_972  -0.1923     1
>      F29   opls_972  -0.1923     1
>      F30   opls_972  -0.1923     1
>      F31   opls_972  -0.1923     1
>      F32   opls_972  -0.1923     1
>      C9    opls_966   0.3846     1
>      C10   opls_966   0.3846     1
>      C11   opls_966   0.3846     1
>      C12   opls_966   0.3846     1
>      F33   opls_972  -0.1923     1
>      F34   opls_972  -0.1923     1
>      F35   opls_972  -0.1923     1
>      F36   opls_972  -0.1923     1
>      F37   opls_972  -0.1923     1
>      F38   opls_972  -0.1923     1
>      F39   opls_972  -0.1923     1
>      F40   opls_972  -0.1923     1
>      C13   opls_966   0.3846     1
>      C14   opls_966   0.3846     1
>      C15   opls_967   0.3218     1
>      C16   opls_966   0.3846     1
>      F41   opls_972  -0.1923     1
>      F42   opls_972  -0.1923     1
>      F43   opls_972  -0.1923     1
>      F44   opls_972  -0.1923     1
>      F45   opls_973  -0.1641     1
>      F46   opls_972  -0.1923     1
>      F47   opls_972  -0.1923     1
>      C48   opls_968   0.3228     1
>      O49   opls_980  -0.2742     1
>      C50   opls_969   0.401      1
>      O51   opls_981  -0.2604     1
>      C52   opls_967   0.3218     1
>      C53   opls_971   0.3216     1
>      F55   opls_974  -0.1637     1
>      F56   opls_974  -0.1637     1
>      F57   opls_975  -0.1932     1
>      C58   opls_970   0.4947     1
>      F59   opls_977  -0.1662     1
>      F60   opls_977  -0.1662     1
>      F61   opls_978  -0.3278     1
>      F62   opls_978  -0.3278     1
>      F66   opls_976  -0.1649     1
>      F67   opls_976  -0.1649     1
>      F68   opls_976  -0.1649     1
>      S54   opls_979   1.4124     1
>      O63   opls_982  -0.632      1
>      O64   opls_982  -0.632      1
>      O65   opls_982  -0.632      1
>

Note that assigning all atoms to a single charge group is inappropriate.
 Surely grompp will warn about this, but you should construct the groups
more carefully.

<snip>

----------------

> However, the parameters that we had in topol file are different:
>
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     2     1
>     1     5     1
>
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2
>    c3
>     2     1     5     1
>     2     1     6     1
>     5     1     6     1
> --------------------------------
>
> How gromacs can find c0, c1,c2 and c3 from b0, kb, th0, and cth in the
> ffbonded.itp?
>
>
I answered this already:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-December/086118.html

You provide the parameters in ffbonded.itp, grompp goes and finds them.  If
something is missing, grompp fails.

-Justin

-- 

==========================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==========================================
-- 
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.