[gmx-users] parameters problem
Nidhi Katyal
nidhikatyal1989 at gmail.com
Tue Mar 11 11:32:43 CET 2014
Thanks Mark. Yes, my ligand.itp indeed has both [atomtypes] entry as well
as [molecule] entry. I have followed the following procedure to #include
while creating my first molecule:
Run pdb2gmx command.
Added #include "ligand.itp" after
#include "charmm27.ff/forcefield.itp"
but before
[ moleculetype ]
; Name nrexcl
Protein_chain_A 3
and added at the end:
[ molecules ]
; Compound #mols
Protein_chain_A 1
LIG 1
SOL 17063
then I have merged protein and ligand coordinates by inserting ATOM lines
from ligand.pdb to *.pdb generated after pdb2gmx command.
Then. I run editconf, genbox and finally grompp command.
After which I got following error:
Fatal error:
No such moleculetype LIG
My both *.itp and *.pdb files contains LIG.
How to rectify the error? Thanks in advance.
On Tue, Mar 11, 2014 at 1:39 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:
> 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
> > >>>
> > >>> * Please search the archive at http://www.gromacs.org/
> > >>> Support/Mailing_Lists/GMX-Users_List before 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 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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