[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
James Starlight
jmsstarlight at gmail.com
Tue Dec 11 12:04:04 CET 2012
Peter, thanks for explanations!
Could you tell me is it possible to convert CGenFF output for
hetatomic group to the RTP (not an itp ) gromac's data ?
I want to simulate in Gromacs ( in charmm 27 ff) qm\mm GFP protein
which is consist of HETTATOMIC chromophore covently bonded to the
polypeptide chain of that protein so
I need topology for that chromophore ( I can make it by swiss param
or my CGenFF) but I need that topology in the rtp file format to
integrate it to the aminoacids.rtp of the Charmm27 for further
processing of the entirely GFP by means of pdb2gmx.
2012/12/8, Peter C. Lai <pcl at uab.edu>:
> 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
>> >>>>>
>> >>>>> ========================================
>> >>>>> --
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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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