AMBER Archive (2009)

Subject: [AMBER] Problem with modified trna[Fwd: problem with creation of prmtop and prmcrd files]]

From: moitrayee_at_mbu.iisc.ernet.in
Date: Mon Jun 08 2009 - 09:30:21 CDT

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_at_mbu.iisc.ernet.in
Date: Mon, June 8, 2009 6:30 pm
To: amber_at_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

  • application/octet-stream attachment: AET.in

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