Thank you for your reply.
Is there any way to generate (.prmtop) and (.incprd) file from (.psf) file?
Thank you.
Sincerely,
Pinky
On Thu, Oct 29, 2020 at 12:34 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> If the only difference is residue names, you can either create a residue
> map in leap config, or e.g. use 'sed' to change residue names in the
> PDB. Atom names can be mapped as well if different.
>
> If a residue isn't in a library, see the paper for the lib for the way
> to get the params to go with the residue template you'll create.
>
>
> On 10/29/20 9:54 AM, Pinky Mazumder wrote:
> > Dear Dr. David,
> >
> > Thanks for your response. I have made cellulose crystals using a toolkit
> > named *cellulose builder *(
> > https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.22959)*.*
> >
> > After that, when I have imported those crystals in xleap (AMBER), it says
> > that the residues are not in the residue templates of AMBER.
> >
> > Is there any method, so that I can change the residue names what is known
> > to AMBER, or is there any way to generate *(.prep) files, (.lib) files*?
> > When I have used cellulose builder, I got* (.pdb) and (.psf) files *as an
> > output.
> >
> > So, How could I solve this issue?
> >
> > Any suggestions would be appreciated.
> >
> > Thank you!
> >
> > Sincerely,
> > Pinky
> >
> > On Thu, Oct 29, 2020 at 7:05 AM David A Case <david.case.rutgers.edu>
> wrote:
> >
> >> On Thu, Oct 29, 2020, Pinky Mazumder wrote:
> >>> Can I built a cellulose crystal structure using AMBER?
> >> Amber is not a model-building program, so you would need to look
> >> elsewhere. But cellulose is a tricky problem, and aspects of its
> >> crystal structure are still unclear. Do an internet search on
> >> "cellulose crystal structure", and you will get lots of good hits. Take
> >> the result that appeals to you most as your starting structure.
> >>
> >> ...good luck...dac
> >>
> >>
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> >>
> >
> --
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--
Pinky, Sharmi
AL,US
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Received on Thu Dec 10 2020 - 23:00:03 PST
