[gmx-users] Regarding Beta-alanine structure

[Dilip H N]

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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Re: [gmx-users] Regarding Beta-alanine structure

[Mark Abraham]

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  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
>
>
>
>  Sent with Mailtrack
> <
> https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality
> >
> --
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Re: [gmx-users] Regarding Beta-alanine structure

[Dilip H N]

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 HGP20.330 !0.000
ATOM H2 HGP20.330 !0.000
ATOM H3 HGP20.330 !0.000
ATOM H4 HGA20.090 !2.500
ATOM H5 HGA20.090 !2.500
ATOM H6 HGA20.090 !0.000
ATOM H7 HGA20.090 !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 CR1  LIG C1   2  0.5030  12.0110
   3 CR1  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.   1.0079
  11 HCMM 1  LIG H5 11  0.   1.0079
  12 HCMM 1  LIG H6 12  0.   1.0079
  13 HCMM 1  LIG H7 13 -0.   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 
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 
> 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
> >
> >
> >
> >  Sent with Mailtrack
> > <
> > https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/
> ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_
> medium=signature&utm_campaign=signaturevirality
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
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>



-- 
With Best Regards,

DILIP.H.N
Ph.D Student
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