[gmx-users] Use dihedraltype 4 to allow several multiplicity terms

[Mark Abraham]

Hi,

Thanks Justin. If you think it useful, then in the CHARMM36 forcefield.itp
you could do stuff like

#if (defined _FF_GROMOS96) || ...
#error Do not attempt to mix another force field with CHARMM36, it is
self-contained
#endif

getting the magic strings from the other share/top/*/forcefield.itp files.
Or does this make sense to do generally, e.g. by giving grompp the smarts
to refuse to #include another forcefield.itp file (or maybe refuse to let
another distinct _FF_* to be #defined)? That doesn't stop people going
directly to "#include ffbonded.itp," but you can't save every lemming... :-)

Mark

On Tue, May 5, 2015 at 3:16 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/5/15 8:09 AM, A. mohammadzadeh wrote:
> > i used output file that made by charmm-gui for gromacs  but gave me the
> > same error.
> >
>
> For the purpose of completing the thread:  Do not modify any topology file
> provided by CHARMM-GUI.  In this case, the OP #included another force
> field and
> broke the format.  CHARMM-GUI provides self-consistent force field files
> that
> rely on nothing else.
>
> -Justin
>
> > On Tue, May 5, 2015 at 4:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 5/5/15 7:35 AM, A. mohammadzadeh wrote:
> >>
> >>> Hello. i have a problem  could you help me to
> >>> solve it pleas?
> >>>
> >>>
> >>> i used charmm server to get the parameters for my new membrane with
> dppc
> >>> and cholestrol -
> >>>
> >>> i converted it into the gromacs topology.
> >>>
> >>>
> >> What does "converted" mean?  I'm assuming you're using CHARMM-GUI, but
> >> that means you don't need any conversion.  We provide all of the inputs
> >> (.mdp, coordinates, topology) that should be used directly.
> >>
> >>   When I try grompp:
> >>>
> >>>
> >>> WARNING 23 [file charmm36.itp, line 41]:
> >>> Overriding atomtype SOD
> >>>
> >>>
> >>> WARNING 24 [file charmm36.itp, line 201]:
> >>> Overriding non-bonded parameters,
> >>>
> >>> old: 0.290767 0.0906104 0.290767 0.0906104 new
> >>> CTL1 SOD 1 2.94954293108e-01 9.06104103511e-02
> >>>
> >>> WARNING 25 [file charmm36.itp, line 222]:
> >>> Overriding non-bonded parameters,
> >>>
> >>> old: 0.290767 0.0906104 0.290767 0.0906104 new
> >>> CTL2 SOD 1 2.94954293108e-01 9.06104103511e-02
> >>>
> >>> WARNING 26 [file charmm36.itp, line 242]:
> >>> Overriding non-bonded parameters,
> >>>
> >>> old: 0.290767 0.0906104 0.290767 0.0906104 new
> >>> CTL3 SOD 1 2.94954293108e-01 9.06104103511e-02
> >>>
> >>> WARNING 27 [file charmm36.itp, line 261]:
> >>> Overriding non-bonded parameters,
> >>>
> >>> old: 0.290767 0.0906104 0.290767 0.0906104 new
> >>> CTL5 SOD 1 2.94954293108e-01 9.06104103511e-02
> >>>
> >>> WARNING 28 [file charmm36.itp, line 498]:
> >>> Overriding Proper Dih. parameters.
> >>> Use dihedraltype 4 to allow several multiplicity terms.
> >>>
> >>> old: 180 4.184 1 180 4.184 1
> >>> new: CEL1 CEL1 CTL2 CEL1 9 0.000000e+00 4.016640e-01 4
> >>>
> >>>
> >> The solution to the problem depends on what you mean by "converted"
> above.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
> >> --
> >> Gromacs Users mailing list
> >>
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> >> posting!
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> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
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