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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Thu Oct 29 2020 - 11:00:03 PDT
