The lib files you created do not specify atom types, charges or even
connectivity for your custom residue. They cannot be used as they are.
Follow the instructions in this tutorial
http://ambermd.org/tutorials/basic/tutorial5/index.htm
to create custom residue lib files. You need to generate charges and
specify atom types, as well as bonding and other parameters. You can use
antechamber to get you started.
Cheers
Pietro
On 14/5/19 3:57 PM, Schröder, David Christopher wrote:
> Dear Amber users,
>
> I was following Tutorial A1 (http://ambermd.org/tutorials/advanced/tutorial1_orig/section1.htm)
> to model a cyclic peptide containing a para connected benzoicacid moiety at C7 position of a tryptophan.
> The sequence is as following: cyclo Trp (7-4Benzoic acid) VAL ARG GLY ASP
> I took a pdb file of the molecule with initial coordinates and cut off the modified Trp and the benzoic acid part, renamed all atoms
> and created from these fragment-pdbs lib files following the tutorial. Please find the files attached.
> When I load these lib files in leap they are not listed when using the list command, furthermore the sequence
> command also does not work.
> I would be grateful for some help. It might be important to note that I am kind of new to amber in general.
>
> Best regards,
> David
>
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Received on Tue May 14 2019 - 02:30:02 PDT
