when I am doing the same step. It could not find force field parameter in
library even i make frcmod file from parmchk.
I have done another approach i have modified name ROH and 0GA in pdb file
and start tleap and they have created structure
ATOM 15834 HO1 ROH 1037 12.641 6.716 -26.264 1.00 0.00
ATOM 15835 O1 ROH 1037 13.154 6.950 -25.479 1.00 0.00
ATOM 15836 C1 0GA 1038 12.493 7.961 -24.799 1.00 0.00
ATOM 15837 H1 0GA 1038 12.905 7.987 -23.790 1.00 0.00
ATOM 15838 C2 0GA 1038 10.973 7.758 -24.733 1.00 0.00
ATOM 15839 H2 0GA 1038 10.792 6.716 -24.464 1.00 0.00
ATOM 15840 C3 0GA 1038 10.324 8.660 -23.655 1.00 0.00
ATOM 15841 H3 0GA 1038 9.423 9.125 -24.061 1.00 0.00
ATOM 15842 C4 0GA 1038 11.291 9.745 -23.176 1.00 0.00
ATOM 15843 H4 0GA 1038 10.808 10.260 -22.343 1.00 0.00
ATOM 15844 C5 0GA 1038 12.648 9.178 -22.708 1.00 0.00
ATOM 15845 H5 0GA 1038 13.389 9.961 -22.882 1.00 0.00
ATOM 15846 C6 0GA 1038 12.726 8.757 -21.242 1.00 0.00
ATOM 15847 H62 0GA 1038 12.289 9.521 -20.598 1.00 0.00
ATOM 15848 H61 0GA 1038 12.171 7.830 -21.090 1.00 0.00
ATOM 15849 O6 0GA 1038 14.098 8.562 -20.836 1.00 0.00
ATOM 15850 H6O 0GA 1038 14.512 9.412 -20.672 1.00 0.00
ATOM 15851 O5 0GA 1038 12.993 8.012 -23.470 1.00 0.00
ATOM 15852 O4 0GA 1038 11.521 10.698 -24.246 1.00 0.00
ATOM 15853 H4O 0GA 1038 10.654 10.973 -24.576 1.00 0.00
ATOM 15854 O3 0GA 1038 9.950 7.838 -22.518 1.00 0.00
ATOM 15855 H3O 0GA 1038 9.549 7.029 -22.866 1.00 0.00
ATOM 15856 O2 0GA 1038 10.345 7.998 -26.034 1.00 0.00
ATOM 15857 H2O 0GA 1038 10.762 8.763 -26.452 1.00 0.00
but again geometry is not correct anomeric OH grup is not bind with
carbon(C1).
please let me know how make a glucose structure with anomeric OH group*.*
On Sun, Sep 10, 2017 at 11:32 PM, Hector A. Baldoni <hbaldoni.unsl.edu.ar>
wrote:
> Hello,
>
> In tleap you would:
>
> tleap -s -f leaprc.GLYCAM_06j-1
> GLU = sequence { ROH 0GB }
> check GLU
> saveamberparm GLU GLU.parm7 GLU.rst7
> saveoff GLU GLU.lib
> saveMol2 GLU GLU.mol2 1
> savepdb GLU GLU.pdb
> quit
>
> Greeting,
> Hector.
>
> PS: http://glycam.org/docs/forcefield/glycam-naming-2/
>
>
> > Dear sir
> >
> > I have checked naming in amber manual but i didn't understand i have also
> > checked naming in GLYCAM_06j-1.prep file but they showed only 0GA,1GA,2GA
> > type but how can i put only single complete GLUCOSE.
> >
> > On Sun, Sep 10, 2017 at 8:36 AM, Elvis Martis <elvis.martis.bcp.edu.in>
> > wrote:
> >
> >> Hi ,
> >> There are specific residue names for each monosaccharide as defined by
> >> GLYCAM FF.
> >> Just see the manual what is the residue name for your case.
> >>
> >> Best Regards
> >> Elvis Martis
> >> Mumbai, INDIA.
> >>
> >> ________________________________________
> >> From: Aashish Bhatt <aashish.ph16221.inst.ac.in>
> >> Sent: 09 September 2017 20:32
> >> To: amber.ambermd.org
> >> Subject: [AMBER] Regarding Glucose naming
> >>
> >> Dear Sir/Ma"am
> >>
> >> I have problem in naming of monosaccharide. I have used name of Glucose
> >> as
> >> GLC. and also supplied leaprc.GLYCAM_06j-1 file. but it did not
> >> recognize.
> >> please let me know if there is any other way of giving GLC as input.
> >>
> >>
> >> Thanking you
> >>
> >> Aashish Bhatt
> >> Institute of nanoscience and technology
> >> Mohali, India
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --------------------------------------
> Dr. Hector A. Baldoni
> Profesor Adjunto (FQByF-UNSL)
> Investigador Adjunto (IMASL-CONICET)
> Area de Quimica General e Inorganica
> Universidad Nacional de San Luis
> Chacabuco 917 (D5700BWS)
> San Luis - Argentina
> hbaldoni at unsl dot edu dot ar
> Tel.:+54-(0)266-4520300 ext. 6157
> --------------------------------------
> -.First thinghs first, but not necesarily in that order.-
>
> -.The theoretical approach these days can predict/show almost anything,
> but the ultimate truth lies in the experiment.-
>
>
> _______________________________________________
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>
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Received on Tue Sep 12 2017 - 08:30:03 PDT
