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. <https://mailtrack.io/> Sent with Mailtrack <https://chrome.google.com/webstore/detail/mailtrack-for-gmail-inbox/ndnaehgpjlnokgebbaldlmgkapkpjkkb?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality> On Thu, Feb 8, 2018 at 1:37 PM, Mark Abraham <mark.j.abra...@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.di...@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 > > > > > > > > <https://mailtrack.io/> 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! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * 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. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * 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. > -- With Best Regards, DILIP.H.N Ph.D Student -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * 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.