[gmx-users] Need to confirm parameters.
Justin Lemkul
jalemkul at vt.edu
Mon May 22 20:35:23 CEST 2017
On 5/22/17 10:00 AM, Sailesh Bataju wrote:
> Hi Sir,
>
> Right, CHARMM force field is what I'm looking for. Thank you very much
> sir for your advice. I've made parameter file of isobutane using
> CHARMM36 force field files shown below so I've a few questions
> regarding it.
>
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 1 yes 1.0 1.0
>
> [ atomtypes ]
> ; name at.num mass charge ptype sigma epsilon
> CC31A 6 12.011000 -0.090 A 0.356359487256 0.13389
> CC33A 6 12.011000 -0.270 A 0.363486677001 0.32635
> HCA1A 1 1.008000 0.090 A 0.238760856462 0.18828
> HCA3A 1 1.008000 0.090 A 0.238760856462 0.10042
>
> [ moleculetype ]
> ; Name nrexcl
> isobutane 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> ; residue 1 IBUT rtp IBUT q 0.0
> 1 CC33A 1 IBUT C1 1 -0.270 ; qtot
> -0.270
> 2 HCA3A 1 IBUT H2 2 0.090 ; qtot -0.180
> 3 HCA3A 1 IBUT H3 3 0.090 ; qtot -0.090
> 4 HCA3A 1 IBUT H4 4 0.090 ; qtot 0.000
> 5 CC31A 1 IBUT C5 5 -0.090 ; qtot -0.090
> 6 HCA1A 1 IBUT H6 6 0.090 ; qtot 0.000
> 7 CC33A 1 IBUT C7 7 -0.270 ; qtot -0.270
> 8 HCA3A 1 IBUT H8 8 0.090 ; qtot -0.180
> 9 HCA3A 1 IBUT H9 9 0.090 ; qtot -0.090
> 10 HCA3A 1 IBUT H10 10 0.090 ; qtot 0.000
> 11 CC33A 1 IBUT C11 11 -0.270 ; qtot -0.270
> 12 HCA3A 1 IBUT H12 12 0.090 ; qtot -0.180
> 13 HCA3A 1 IBUT H13 13 0.090 ; qtot -0.090
> 14 HCA3A 1 IBUT H14 14 0.090 ; qtot 0.000
>
> [ bonds ]
> : ai aj funct b0(nm) kb[KJ mol^(-1) nm^(-2)] ; 13 bonds
> 1 2 1 0.11110000 269449.60
> 1 3 1 0.11110000 269449.60
> 1 4 1 0.11110000 269449.60 ;
> C13
> 1 5 1 0.15380000 186188.00 ;
> |
> 5 6 1 0.11110000 258571.20 ;
> H14--C11--H12
> 5 7 1 0.15380000 186188.00 ;
> |
> 5 11 1 0.15380000 186188.00 ;
> H2 | H8
> 7 8 1 0.11110000 269449.60 ;
> | | |
> 7 9 1 0.11110000 269449.60 ;
> H3--C1--C5--C7--H9
> 7 10 1 0.11110000 269449.60 ;
> | | |
> 11 12 1 0.11110000 269449.60 ;
> H4 H6 H10
> 11 13 1 0.11110000 269449.60 ;
> 11 14 1 0.11110000 269449.60
>
> [ pairs ]
> ; ai aj funct ; 27 pairs
> 1 8 1
> 1 9 1
> 1 10 1
> 1 12 1
> 1 13 1
> 1 14 1
> 2 6 1
> 2 7 1
> 2 11 1
> 3 6 1
> 3 7 1
> 3 11 1
> 4 6 1
> 4 7 1
> 4 11 1
> 6 8 1
> 6 9 1
> 6 10 1
> 6 12 1
> 6 13 1
> 6 14 1
> 7 12 1
> 7 13 1
> 7 14 1
> 8 11 1
> 9 11 1
> 10 11 1
>
> [ angles ]
> ; ai aj ak funct theta0(deg) ktheta(KJ mol^(-1) rad^(-2))
> ub0(nm) kub(KJ mol^(-1) nm^(-2)) ; 24 angles
> 2 1 3 5 108.400000 297.064000
> 0.18020000 4518.72 ; HCA3A-CC33A-HCA3A
> 2 1 4 5 108.400000 297.064000
> 0.18020000 4518.72
> 3 1 4 5 108.400000 297.064000
> 0.18020000 4518.72
> 8 7 9 5 108.400000 297.064000
> 0.18020000 4518.72
> 8 7 10 5 108.400000 297.064000
> 0.18020000 4518.72
> 9 7 10 5 108.400000 297.064000
> 0.18020000 4518.72
> 12 11 13 5 108.400000 297.064000
> 0.18020000 4518.72
> 12 11 14 5 108.400000 297.064000
> 0.18020000 4518.72
> 13 11 14 5 108.400000 297.064000
> 0.18020000 4518.72
> 5 1 2 5 110.100000 279.742240
> 0.21790000 18853.10 ; CC31A-CC33A-HCA3A
> 5 1 3 5 110.100000 279.742240
> 0.21790000 18853.10
> 5 1 4 5 110.100000 279.742240
> 0.21790000 18853.10
> 5 7 8 5 110.100000 279.742240
> 0.21790000 18853.10
> 5 7 9 5 110.100000 279.742240
> 0.21790000 18853.10
> 5 7 10 5 110.100000 279.742240
> 0.21790000 18853.10
> 5 11 12 5 110.100000 279.742240
> 0.21790000 18853.10
> 5 11 13 5 110.100000 279.742240
> 0.21790000 18853.10
> 5 11 14 5 110.100000 279.742240
> 0.21790000 18853.10
> 7 5 6 5 110.100000 288.696000
> 0.21790000 18853.10 ; CC33A-CC31A-HCA1A
> 1 5 6 5 110.100000 288.696000
> 0.21790000 18853.10
> 11 5 6 5 110.100000 288.696000
> 0.21790000 18853.10
> 1 5 7 5 114.000000 446.432800
> 0.25610000 6694.40 ; CC33A-CC31A-CC33A
> 1 5 11 5 114.000000 446.432800
> 0.25610000 6694.40
> 11 5 7 5 114.000000 446.432800
> 0.25610000 6694.40
>
> [ dihedrals ]
> ; ai aj ak al funct phi0(deg) kphi(KJ mol^(-1))
> mult ; 27 dihedrals
> 2 1 5 6 9 0.000000 0.836800 3
> ; HCA1A-CC31A-CC33A-HCA3A
> 2 1 5 7 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 2 1 5 11 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 3 1 5 6 9 0.000000 0.836800 3
> ; HCA1A-CC31A-CC33A-HCA3A
> 3 1 5 7 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 3 1 5 11 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 4 1 5 6 9 0.000000 0.836800 3
> ; HCA1A-CC31A-CC33A-HCA3A
> 4 1 5 7 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 4 1 5 11 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 1 5 7 8 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 1 5 7 9 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 1 5 7 10 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 6 5 7 8 9 0.000000 0.836800 3
> ; HCA1A-CC31A-CC33A-HCA3A
> 6 5 7 9 9 0.000000 0.836800 3
> ; HCA1A-CC31A-CC33A-HCA3A
> 6 5 7 10 9 0.000000 0.836800 3
> ; HCA1A-CC31A-CC33A-HCA3A
> 11 5 7 8 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 11 5 7 9 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 11 5 7 10 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 1 5 11 12 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 1 5 11 13 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 1 5 11 14 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 6 5 11 12 9 0.000000 0.836800 3
> ; HCA1A-CC31A-CC33A-HCA3A
> 6 5 11 13 9 0.000000 0.836800 3
> ; HCA1A-CC31A-CC33A-HCA3A
> 6 5 11 14 9 0.000000 0.836800 3
> ; HCA1A-CC31A-CC33A-HCA3A
> 7 5 11 12 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 7 5 11 13 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
> 7 5 11 14 9 0.000000 0.836800 3
> ; CC33A-CC31A-CC33A-HCA3A
>
>
> 1. In [pairs] section I've kept it empty and made gen-pairs yes at
> [defaults] section does it generates the value automatically? If yes,
> is that a safe way to do it or fill up the parameters by myself?
>
gen-pairs has to do with generating the parameters for the listed pairs. If
you've got no listed pairs, then nothing will be done. That's incorrect.
> 2. Please see those parameters I've chosen and point out the errors if
> I've made. I don't know if some more sections are to be added here.
>
I'm not going to go line by line and check your work. The easiest thing to do
(solving this issue and #1) is to create an isobutane .rtp entry and have
pdb2gmx do all the work for you. It's very simple to do.
-Justin
> Thank you very much.
>
>
>> At minimum, some all-atom force field, because whatever you were doing before
>> has no relationship to GROMOS and is unlikely to succeed.
>
>> Isobutane is just the valine side chain, so that's certainly a model compound in
>> existing force fields and should have parameters published and validated for any
>> of the major all-atom force fields. I know it's in CHARMM, and certainly others.
>
>> Justin
>
>
> On Fri, May 19, 2017 at 6:07 PM, Sailesh Bataju <thelaven at gmail.com> wrote:
>
>> Hi Sir,
>>
>> You mean like choosing OPLS forcefield for all-atom model would be moer
>> appropriate for me?
>>
>> Thank you.
>>
>> On Fri, May 19, 2017 at 5:15 PM, Sailesh Bataju <thelaven at gmail.com>
>> wrote:
>>
>>> Hi Sir/Ma'am,
>>>
>>> I've finally created parameter file of isobutane using gromos54a7
>>> forcefield for all-atom model. Some of the parameters for bond angle
>>> parameters like H-C-H and C-C-H bond angle were not found in ffbonded.itp
>>> file in the relevant forcefield, instead I used FTFE - CTFE - FTFE and
>>> CLChl - CChl - CLChl respectively which i found it in the sample of the
>>> file generated by https://atb.uq.edu.au/ website. Somehow luckily found
>>> corresponding bond angle approximately equivalent to the experimental data
>>> observed but didn't find the bond angle constant in experimental data.
>>> Therefore I'm not sure if I can trust the parameter selected.
>>>
>>> I need your advice to help me decide to go further.
>>> Thank you very much.
>>>
>>> --
>>> Self-reliant is the great potential for success.
>>>
>>
>>
>>
>> --
>> Self-reliant is the great potential for success.
>>
>
>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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