[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
James Starlight
jmsstarlight at gmail.com
Tue Dec 11 22:13:43 CET 2012
Today I've made parametrization of the chromophore group by means of
Swiss param and integrated that topology into charmm27 ff. The only
problem that I have is with the N-term N atom of the chromophore. It's
likely that I made mistake to parametrize it into full protonated form
(NH2).
When I've used pdb2gmx on the GFP structure the peptide bond between
that N atom and adjacent O ( from C term of adjacent residue) is
incorrect ( both oxygens preserves on the C atom so my system had
divided onto 2 chains as well as had incorrect charge). How I could
define the N atom in the topology as the N-terminal? (I've delited
both hydrogens from RTP as well as from HDB files but the problem
didn’t resolved. Also I'm using -ignh on the input pdb to ignore all
hydrogens from the model)
James
2012/12/11, Justin Lemkul <jalemkul at vt.edu>:
>
>
> On 12/11/12 6:04 AM, James Starlight wrote:
>> 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.
>>
>
> You've repeated this request several times now, and the answer is always the
>
> same. If you have suitable parameters in some form, they need to be
> converted
> to Gromacs format (.rtp) by some means. If you haven't found or written
> some
> program that converts the formats, the only solution is to fire up your
> favorite
> text editor, open up the Gromacs manual, and get typing. The .rtp format is
>
> relatively straightforward, and you will probably be better served if you
> try to
> write one and post back with specific questions if you have specific
> problems
> getting it to work.
>
> Note that suitable parameters for the GFP chromophore are published (and
> that
> paper was linked before in this discussion), so you likely do not need to
> re-derive any of these parameters using SwissParam or CGenFF. A few years
> ago,
> we used the published CHARMM27-compatible parameters in a set of GFP
> simulations.
>
> -Justin
>
>> 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
>>>>>>>>>
>>>>>>>>> ========================================
>>>>>>>>> --
>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>>>>>>> posting!
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>>>>>>>>> www interface or send it to gmx-users-request 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
>>>>>>>
>>>>>>> ========================================
>>>>>>> --
>>>>>>> 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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