[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
Peter C. Lai
pcl at uab.edu
Sat Dec 8 13:35:56 CET 2012
On 2012-12-08 03:20:54AM -0800, James Starlight wrote:
> 1- on what assumptions that blocks were generated ?
This appears to be a swissparm-specific question. I don't know what
algorithms it uses to match what are essentially pharmacophores in the new
molecule with the common individual blocks it finds.
> 2- Why charge in [ atomtypes ] (zero) differes from the charges in
Because gromacs ignores charges in [atomtypes], so the easiest thing is to
just assign all zeros to that column.
> the topology of the same groups? how I can check correctness of charge
> distribution in such itp files ?
Compare to analogous molecules and see if there are published charges.
You can also use the building blocks and manually assign charges and see what
you end up with as well. To be totally rigorous, parameterize the structure
using a quantum chemistry package and compare the ab initio charge
distributions to the ones assigned by SwissParm (or by hand).
> 3- What is sigma and epsilon in the [ atomtypes ] ? :)
LJ interactions in sigma-epsilon form. See gromacs manual section 4.1.1
> 4- Have anybody else used Swiss param for modeling protein-ligands
> systems? Might it be used with the charmm36 set ?
>
CHARMM has its own generalized forcefield (CGenFF) for ligands and other
molecules, although charmm36 may have cAMP in their nucleotides section...
You can try to also build it using adenine, ribose, and add phosphate.
CGenFF and C36 are interoperable for intermolecular interactions, so if
using CGenFF to paramterize cAMP you would use ParamChem to assign charges
and then convert and add the CGenFF forcefield parameters (from the gromacs
contributions website) to C36. There are mailing list archives that show
you the script to use to do the CGenFF conversion.
> James
>
> 2012/12/7, Justin Lemkul <jalemkul at vt.edu>:
> >
> >
> > On 12/7/12 2:21 PM, James Starlight wrote:
> >> Justin,
> >>
> >> with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2
> >> rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp
> >>
> >> NOTE 1 [file ./mdps/em.mdp]:
> >> For energy conservation with switch/shift potentials, rlist should be
> >> 0.1
> >> to 0.3 nm larger than rvdw.
> >>
> >> NOTE 2 [file ./mdps/em.mdp]:
> >> The sum of the two largest charge group radii (0.078024) is larger
> >> than
> >> rlist (1.200000) - rvdw (1.200000)
> >>
> >
> > As I recall, there is a small bug where grompp ignores rlistlong when
> > printing
> > this message. The simulation will be fine.
> >
> > -Justin
> >
> >>
> >> Should I increase Rlist to the 1.4 ( as well as rcoulomb to the same
> >> value because of PME) ?
> >>
> >> 2012/12/7, Justin Lemkul <jalemkul at vt.edu>:
> >>>
> >>>
> >>> On 12/7/12 1:19 PM, James Starlight wrote:
> >>>> Justin,
> >>>>
> >>>> following to your advise I've tried to use charmm 27 ff for simulation
> >>>> of my protein-cGMP complex ( ligand was parametrized by Swiss Param
> >>>> server).
> >>>>
> >>>> Could you provide me with the cut-offs for vdw as well as
> >>>> electrostatics suitable for simulation in charmm27 and 36 force
> >>>> fields?
> >>>>
> >>>
> >>> http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html
> >>>
> >>>> Does anybody know another servers for parametrization of the ligands
> >>>> for charmm simulation in gromacs?
> >>>>
> >>>
> >>> If Google can't find it, it probably doesn't exist.
> >>>
> >>> -Justin
> >>>
> >>>> 2012/12/7, Justin Lemkul <jalemkul at vt.edu>:
> >>>>>
> >>>>>
> >>>>> On 12/7/12 11:42 AM, James Starlight wrote:
> >>>>>> Justin,
> >>>>>>
> >>>>>> ligand-only simulation in vacuum have been finished with the same
> >>>>>> errors
> >>>>>> :)
> >>>>>>
> >>>>>> Step 19200, time 38.4 (ps) LINCS WARNING
> >>>>>> relative constraint deviation after LINCS:
> >>>>>> rms 0.025443, max 0.140660 (between atoms 1 and 3)
> >>>>>> bonds that rotated more than 30 degrees:
> >>>>>> atom 1 atom 2 angle previous, current, constraint length
> >>>>>> 1 2 52.2 0.1033 0.0985 0.1000
> >>>>>> 1 3 90.1 0.1168 0.1141 0.1000
> >>>>>>
> >>>>>> Step 19200, time 38.4 (ps) LINCS WARNING
> >>>>>> relative constraint deviation after LINCS:
> >>>>>> rms 0.025376, max 0.140474 (between atoms 1 and 3)
> >>>>>> bonds that rotated more than 30 degrees:
> >>>>>> atom 1 atom 2 angle previous, current, constraint length
> >>>>>> 1 2 52.0 0.1033 0.0988 0.1000
> >>>>>> 1 3 90.0 0.1168 0.1140 0.1000
> >>>>>> step 19200, will finish Sat Dec 8 04:10:49 2012
> >>>>>> Step 19201, time 38.402 (ps) LINCS WARNING
> >>>>>> relative constraint deviation after LINCS:
> >>>>>> rms 0.052715, max 0.293316 (between atoms 1 and 3)
> >>>>>> bonds that rotated more than 30 degrees:
> >>>>>> atom 1 atom 2 angle previous, current, constraint length
> >>>>>> 1 2 49.3 0.0988 0.0993 0.1000
> >>>>>> 1 3 90.0 0.1140 0.1293 0.1000
> >>>>>>
> >>>>>> Step 19201, time 38.402 (ps) LINCS WARNING
> >>>>>> relative constraint deviation after LINCS:
> >>>>>> rms 0.052900, max 0.294281 (between atoms 1 and 3)
> >>>>>> bonds that rotated more than 30 degrees:
> >>>>>> atom 1 atom 2 angle previous, current, constraint length
> >>>>>> 1 2 49.6 0.0988 0.0989 0.1000
> >>>>>> 1 3 90.0 0.1140 0.1294 0.1000
> >>>>>>
> >>>>>> Step 19202, time 38.404 (ps) LINCS WARNING
> >>>>>> relative constraint deviation after LINCS:
> >>>>>> rms 0.035783, max 0.198482 (between atoms 1 and 3)
> >>>>>> bonds that rotated more than 30 degrees:
> >>>>>> atom 1 atom 2 angle previous, current, constraint length
> >>>>>> 1 2 33.3 0.0989 0.0984 0.1000
> >>>>>> 1 3 89.9 0.1294 0.1198 0.1000
> >>>>>>
> >>>>>> -------------------------------------------------------
> >>>>>> Program mdrun, VERSION 4.5.4
> >>>>>> Source code file: /tmp/gromacs-4.5.4/src/mdlib/constr.c, line: 176
> >>>>>>
> >>>>>> Fatal error:
> >>>>>> Too many LINCS warnings (1000)
> >>>>>>
> >>>>>>
> >>>>>> ITs intresting that the same files (like step-1c_n11.pdb) have been
> >>>>>> produced already during CG minimisation phase but the system have not
> >>>>>> been crashed. So I suppoe that the problem is in geometry of the
> >>>>>
> >>>>> If you get errors in the minimization, that should indicate that
> >>>>> either
> >>>>> the
> >>>>>
> >>>>> topology or configuration is flawed.
> >>>>>
> >>>>>> mollecule. The direct comparison of the bonds and angles with the rtp
> >>>>>> (DGUA) is non trivial again because of differs in the file formats
> >>>>>> representation :)
> >>>>>>
> >>>>>
> >>>>> Most troubleshooting is not easy. You can also create a topology for
> >>>>> DGUA
> >>>>> from
> >>>>> just about any DNA structure and compare its .top against your cGMP
> >>>>> topology.
> >>>>>
> >>>>> -Justin
> >>>>>
> >>>>> --
> >>>>> ========================================
> >>>>>
> >>>>> Justin A. Lemkul, Ph.D.
> >>>>> Research Scientist
> >>>>> Department of Biochemistry
> >>>>> Virginia Tech
> >>>>> Blacksburg, VA
> >>>>> jalemkul[at]vt.edu | (540) 231-9080
> >>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>>>>
> >>>>> ========================================
> >>>>> --
> >>>>> gmx-users mailing list gmx-users at gromacs.org
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> >>>>>
> >>>
> >>> --
> >>> ========================================
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Research Scientist
> >>> Department of Biochemistry
> >>> Virginia Tech
> >>> Blacksburg, VA
> >>> jalemkul[at]vt.edu | (540) 231-9080
> >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>>
> >>> ========================================
> >>> --
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> >>>
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
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