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

From: Saikat Dutta chowdhury <pbr322.dutta.gmail.com>
Date: Sun, 12 May 2019 12:10:19 +0530

Respected All,
I am trying to simulate a homopolypeptide in explicit solvent condition.
But the amino acid is phosphoglutamate, and I haven't found any parameters
for this. Hence I tried antechamber for getting the parameters. I had built
my polypeptide in Avogadro and followed the "Antechamber Tutorial" to get
the parameters. Then I proceeded to create a system with the polypeptide in
an octahedron box with explicit water using .lib and .frcmod files. I was
able to get the prmtop, inpcrd and pdb files but there are some issues

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.

2. There are two issues I noticed in the tleap output. There are multiple
lines like "Added missing heavy atom: .R<PGU 1>.A<C 291>" and there few
lines with a warning like
WARNING: There is a bond of 3.322174 angstroms between:
------- .R<PGU 1>.A<C51 277> and .R<PGU 1>.A<O 278>

It will be very helpful if anyone can suggest me about how can I prepare
the parameters for the modified amino acid so that I can set up a proper
system for simulation.

With regards,
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
AMBER mailing list
Received on Sun May 12 2019 - 00:00:02 PDT
Custom Search