[gmx-users] Regarding Beta-alanine structure
Dilip H N
cy16f01.dilip at nitk.edu.in
Fri Feb 9 10:01:54 CET 2018
Hello,
I have got the zwitterion structure of beta-alanine from ChEBI website, and
the ChEBI Id is *CHEBI:57966.*
I downloaded in mol2 format and tried with the CGenFF and swissparam servers
to get the charmm FF. but i have got two different charges for each of the
case.
In case of CGenFF the charges i got by uploading the zwitterionic
beta-alanine.mol2:
ESI ***** 0.000 ! param penalty= 4.000 ; charge penalty= 12.737
GROUP ! CHARGE CH_PENALTY
ATOM N NG3P3 -0.299 ! 2.500
ATOM C1 CG324 0.127 ! 10.269
ATOM C2 CG321 -0.245 ! 12.737
ATOM O1 OG2D2 -0.760 ! 0.850
ATOM C3 CG2O3 0.587 ! 12.403
ATOM O2 OG2D2 -0.760 ! 0.850
ATOM H1 HGP2 0.330 ! 0.000
ATOM H2 HGP2 0.330 ! 0.000
ATOM H3 HGP2 0.330 ! 0.000
ATOM H4 HGA2 0.090 ! 2.500
ATOM H5 HGA2 0.090 ! 2.500
ATOM H6 HGA2 0.090 ! 0.000
ATOM H7 HGA2 0.090 ! 0.000
In case of SwissParam the charges i got by uploading the zwitterionic
beta-alanine.mol2:
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 NRP 1 LIG N1 1 -0.8530 14.0067
2 CR 1 LIG C1 2 0.5030 12.0110
3 CR 1 LIG C2 3 -0.1060 12.0110
4 O2CM 1 LIG O1 4 -0.9000 15.9994
5 CO2M 1 LIG C3 5 0.9060 12.0110
6 O2CM 1 LIG O2 6 -0.9000 15.9994
7 HNRP 1 LIG H1 7 0.4500 1.0079
8 HNRP 1 LIG H2 8 0.4500 1.0079
9 HNRP 1 LIG H3 9 0.4500 1.0079
10 HCMM 1 LIG H4 10 0.0000 1.0079
11 HCMM 1 LIG H5 11 0.0000 1.0079
12 HCMM 1 LIG H6 12 0.0000 1.0079
13 HCMM 1 LIG H7 13 -0.0000 1.0079
So, how can i validate that which charges for the molecule, is correct..??
Which one is correct one to run the simulation in gromacs (using charmm36
FF)..??
Any suggestions are appreciated.
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On Thu, Feb 8, 2018 at 1:37 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> You should start with the original literature and/or CHARMM forcefield
> distribution for its documentation. That wasn't ported to the force field
> files one can use with GROMACS.
>
> Mark
>
> On Thu, Feb 8, 2018 at 7:19 AM Dilip H N <cy16f01.dilip at nitk.edu.in>
> wrote:
>
> > Hello,
> > I want to simulate beta-alanine amino-acid. But in charmm36 FF there are
> > four different names (three/four letter code) for ALA, ie., ALA, DALA,
> > ALAI, ALAO.
> > Out of this, i wanted to know which one corresponds to beta-alanine
> > structure..??
> >
> > I tried in Avogadro software and i could build only alanine structure,
> and
> > not beta-alanine. How can i get the pdb file of beta-alanine..?? any
> other
> > ways..?
> > So, can anybody help me regarding this..??
> >
> > Thank you.
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D. Student
> >
> >
> >
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With Best Regards,
DILIP.H.N
Ph.D Student
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