[gmx-users] parameters problem

Mon Mar 10 21:09:49 CET 2014

Probably you will see that your ligand.itp has an [atomtypes] entry as well
as a [molecule] entry, and the former cannot follow any instance of the
latter. Such an .itp file must be #included to create the first molecule.
You have your protein [molecule] above the #include "ligand.itp" at the
moment, which would cause this problem.

Mark

On Mon, Mar 10, 2014 at 7:09 PM, Nidhi Katyal <nidhikatyal1989 at gmail.com>wrote:

> To test swiss param parameters, I have generated *.pdb and *.itp files from
> it. In the genbox command, I have used -ci *.pdb -nmol 2.
> I have included *.itp in the topology as:
>
> ; Include Position restraint file
> ;#ifdef POSRES
> ;#include "posre.itp"
> ;#endif
>
> ;Include ligand topology
> #include "ligand.itp"
>
> ; Include water topology
> #include "charmm27.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "charmm27.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein in water
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> LIG                 2
> SOL             12904
>
> But after I run grompp command, I get following error:
>
> Fatal error:
> Syntax error - File ligand.itp, line 7
> Last line read:
> '[ atomtypes ] '
> Invalid order for directive atomtypes
>
> Please help me rectify the problem of the order getting violated although
> same worked for topology generated by PRODRG.
>
> Thanks in advance.
>
>
>
> On Mon, Mar 10, 2014 at 10:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 3/10/14, 8:21 AM, Nidhi Katyal wrote:
> >
> >> Thanks Justin. I would also like to know the reliability of parameters
> >> generated using swiss param.
> >>
> >>
> >>
> > I have no personal experience with it.  My rule is to never trust
> anything
> > from a black-box server without verifying it and assessing any
> information
> > about penalties, deviations, etc. that it provides.
> >
> > -Justin
> >
> >
> >  On Mon, Mar 10, 2014 at 3:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >>
> >>>
> >>> On 3/10/14, 2:45 AM, Nidhi Katyal wrote:
> >>>
> >>>  Thank you Mark and Justin.
> >>>> Now, I have carried out simulations using PME electrostatics and using
> >>>> all other
> >>>> parameters (except gromos 96 43a1 ff used) as suggested in
> >>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> >>>> gmx-tutorials/lysozyme/
> >>>>
> >>>> The protein is not loosing its structure now. But the problem is if I
> >>>> carry out
> >>>> simulations in the presence of experimentally known stabiliser
> generated
> >>>> using
> >>>> ProDrg (keeping all the parameters same while simulating both in the
> >>>> presence
> >>>> and absence of stabiliser), the partial loss of secondary structure is
> >>>> observed
> >>>> in the presence of stabilizer relative to the case in its absence at
> >>>> 350K
> >>>> thereby implying simulations going against experimental observations
> >>>> (although
> >>>> slight stabilization was observed at 300K). Simulations were repeated
> >>>> twice with
> >>>> two different force fields.
> >>>> However if I use above em,pr,full parameters with cut-off
> >>>> electrostatics,
> >>>> although secondary structure is lost in the initial stages but I could
> >>>> clearly
> >>>> see the stabilization behaviour of additive in terms of secondary
> >>>> structure
> >>>> retainment till longer time. Is this observation a matter of chance-
> >>>> reliable or
> >>>> not? What could be the possible reason for not observing such
> >>>> stabilization with
> >>>> better parameters?
> >>>>
> >>>>
> >>>>  Cutoff electrostatics are horribly inaccurate.  The fact that you
> >>> conveniently see what you hope to when using a plain cutoff is likely
> by
> >>> chance.
> >>>
> >>> The bigger issue is the use of PRODRG parameters.  As I have said
> >>> numerous
> >>> times on this list, the parameters it produces are demonstrably
> >>> inaccurate
> >>> and require reparametrization.
> >>>
> >>> http://pubs.acs.org/doi/abs/10.1021/ci100335w
> >>>
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ==================================================
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Ruth L. Kirschstein NRSA 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
> >>> http://mackerell.umaryland.edu/~jalemkul
> >>>
> >>> ==================================================
> >>> --
> >>> Gromacs Users mailing list
> >>>
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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 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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