On Fri, Dec 13, 2013 at 1:16 PM, Ehsan Sadeghi <es...@sfu.ca> wrote:

> 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.
>
>
Beyond atom numbers, nothing will show up and nothing should show up.  Each
atom number is linked to an atom type (listed in [atoms]).  grompp looks at
the atom numbers in the bonded directives, references the atom types in
[atoms], then goes into ffbonded.itp to see if there is a suitable match
for those parameters.  As long as grompp finds a suitable match, everything
is fine.  If grompp says something is missing, go into the .top file to the
specified line, map back the atom types corresponding to those numbers, and
fix ffbonded.itp as needed.

-Justin


> Kind regards,
> Ehsan
>
> ----- Original Message -----
> From: "Justin Lemkul" <jalem...@vt.edu>
> To: "Discussion list for GROMACS users" <gmx-us...@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 <es...@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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>
>
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-- 

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

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441


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