Hi David,
Actually, I am following antechamber tutorial(
https://ambermd.org/tutorials/basic/tutorial4b/index.html).
I am sorry for missing the system information, “UNL” stands for the name of the ligand.
Actually I am feeding the result of Vina into AMBER and due to some reason the Vina is changing the name of the ligand to “UNL”.
As per given in the above tutorial, I am first creating library & top/parameter file for the ligand(UNL) and then following the tutorial to create top/parameter file for the complex.
And this is where the error shows-up. I am following the same tutorial for another system without any problem, and I followed the same steps here as well.
Thank you.
——
> On Oct 1, 2020, at 4:45 PM, David A Case <david.case.rutgers.edu> wrote:
>
> On Thu, Oct 01, 2020, Jatin Kashyap wrote:
>>
>> I am new to biological simulations. Can anybody please help me to
>> understand why I am getting below error, and how to solve it.
>
> You should tell us more about what you did here. What is "UNL"?
> (Unkown ligand?) Did you do anything to create an Amber library for
> this? If not, check out tutorial 2.1.
>
>>> complex = loadpdb complex_H.pdb
>> Loading PDB file: ./complex_H.pdb
>> -- residue 835: duplicate [ C] atoms (total 18)
>> -- residue 835: duplicate [ N] atoms (total 3)
>
> Atom names in a given residue (residue 835 in this case) need to be
> unique. Take a look at your PDB file. If you are truly beginning with
> Amber, start with a smaller system, and one with no non-standard
> residues. Then build up complexity as you gain experience.
>
> ...hope this helps....dac
>
>
> _______________________________________________
> 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
Received on Thu Oct 01 2020 - 14:00:04 PDT
