[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
James Starlight
jmsstarlight at gmail.com
Sat Dec 8 12:20:54 CET 2012
Today I've performed test simulation of the protein-cAMP complex with
the charmm27 force field and obtain good stable system. I've compared
polar contacts of my complex ( ligand have been done with SwissParam)
with the X-ray structure of that protein solved with the same complex
and obtained similar picture in both cases.
When I've checked ligand's topology produced by Swiss param I noticed
that it was built from some building blocks generated by SwissParam (
and found in the same topology file) with the specified charge
distribution ( the below example is the cAMP mollecule)
; nr type resnr resid atom cgnr charge mass
1 NPYL 1 LIG N9 1 0.0476 14.0067
2 C5A 1 LIG C8 2 0.0365 12.0110
3 N5B 1 LIG N7 3 -0.5653 14.0067
4 C5B 1 LIG C5 4 0.2272 12.0110
5 CB 1 LIG C6 5 0.4100 12.0110
6 NPYD 1 LIG N1 6 -0.6200 14.0067
7 CB 1 LIG C2 7 0.4700 12.0110
8 NPYD 1 LIG N3 8 -0.5670 14.0067
9 C5A 1 LIG C4 9 0.1054 12.0110
10 HCMM 1 LIG H01 10 0.1500 1.0079
11 HCMM 1 LIG H02 11 0.0000 1.0079
12 HCMM 1 LIG H03 12 0.0000 1.0079
13 HCMM 1 LIG H04 13 0.0000 1.0079
14 HCMM 1 LIG H05 14 0.0000 1.0079
15 HOR 1 LIG H06 15 0.4000 1.0079
16 HCMM 1 LIG H07 16 0.0000 1.0079
17 HCMM 1 LIG H08 17 0.1500 1.0079
18 HNCO 1 LIG H09 18 0.4000 1.0079
19 HNCO 1 LIG H10 19 0.4000 1.0079
20 HCMM 1 LIG H11 20 0.0000 1.0079
21 PO4 1 LIG P 21 1.4424 30.9738
22 O2CM 1 LIG O1P 22 -0.9500 15.9994
23 O2CM 1 LIG O2P 23 -0.9500 15.9994
24 OR 1 LIG O5' 24 -0.5512 15.9994
25 CR 1 LIG C5' 25 0.2800 12.0110
26 CR 1 LIG C4' 26 0.2800 12.0110
27 OR 1 LIG O4' 27 -0.5600 15.9994
28 CR 1 LIG C3' 28 0.2800 12.0110
29 OR 1 LIG O3' 29 -0.5512 15.9994
30 CR 1 LIG C2' 30 0.2800 12.0110
31 OR 1 LIG O2' 31 -0.6800 15.9994
32 CR 1 LIG C1' 32 0.5356 12.0110
33 NC=C 1 LIG N6 33 -0.9000 14.0067
where building blocks were
[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
NPYL 7 14.0067 0.0 A 0.306469 0.376560
C5A 6 12.0110 0.0 A 0.363487 0.209200
N5B 7 14.0067 0.0 A 0.329632 0.836800
C5B 6 12.0110 0.0 A 0.363487 0.209200
CB 6 12.0110 0.0 A 0.355005 0.292880
NPYD 7 14.0067 0.0 A 0.329632 0.836800
HCMM 1 1.0079 0.0 A 0.235197 0.092048
HOR 1 1.0079 0.0 A 0.040001 0.192464
HNCO 1 1.0079 0.0 A 0.040001 0.192464
PO4 15 30.9738 0.0 A 0.383086 2.447640
O2CM 8 15.9994 0.0 A 0.302905 0.502080
OR 8 15.9994 0.0 A 0.315378 0.636386
CR 6 12.0110 0.0 A 0.387541 0.230120
NC=C 7 14.0067 0.0 A 0.329632 0.836800
So its interesting for me
1- on what assumptions that blocks were generated ?
2- Why charge in [ atomtypes ] (zero) differes from the charges in
the topology of the same groups? how I can check correctness of charge
distribution in such itp files ?
3- What is sigma and epsilon in the [ atomtypes ] ? :)
4- Have anybody else used Swiss param for modeling protein-ligands
systems? Might it be used with the charmm36 set ?
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
>>>
>>> ========================================
>>> --
>>> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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