Re: [AMBER] Problem with preparing parameters with antechamber for modified amino acid

From: Saikat Dutta chowdhury <pbr322.dutta.gmail.com>
Date: Mon, 13 May 2019 13:16:40 +0530

Thank you for your reply.
I have used both pymol and vmd for viewing the molecule.

with regards,
Saikat

On Sun, May 12, 2019 at 2:23 PM Bill Ross <ross.cgl.ucsf.edu> wrote:

> On 5/11/19 11:40 PM, Saikat Dutta chowdhury wrote:
> > 1. When I am opening the pdb files for the system I found out that the
> > phosphate moieties are no longer attached to the amino acids.
>
> What viewer? Likely it's seeing a residue it doesn't know the bonding
> of, since it's an unknown res name.
>
> Bill
>
>
>
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-- 
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
Mob:
8017650842
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Received on Mon May 13 2019 - 01:00:01 PDT
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