Dear Amber Users,
Probing a little further in the problem described below, I have found that if I
remove the modified trna residue AET from the pdb file as attached, there is no
problem in creating the topology and coordinate files. The prepi file that I am
using for AET has been created using antechamber from the Gaussian optimization
output. I am attaching the prepi file.
Also during the use of the antechamber to generate the desired prepi file, there
is a warning showing:
"The number of the ESP exceeds the MAXESP(20000),extend the size and reallocate
the memory"
Can this cause a problem?
Please help me with this problem.
Sincere Regards
Moitrayee Bhattacharyya
Molecular Biophysics Unit
Indian Institute of Science
Bangalore - 560 012
India
------------------------------- Original Message -------------------------------
Subject: problem with creation of prmtop and prmcrd files
From: moitrayee.mbu.iisc.ernet.in
Date: Mon, June 8, 2009 6:30 pm
To: amber.ambermd.org
--------------------------------------------------------------------------------
Dear Amber Users,
I am trying to generate the topology and coordinate files for a protein
complexed with trna and ligand. I am getting the following error as attached in
the file: error_file. I am also attaching the original pdb file.
Please suggest me with a solution.
Thanks and Regards,
Moitrayee Bhattacharyya
Molecular Biophysics Unit
Indian Institute of Science
Bangalore - 560 012
India
- application/octet-stream attachment: prot.pdb
Received on Tue Jun 09 2009 - 01:10:03 PDT
