[AMBER] Residuegen Usage

From: Seungyeul Yoo <Seungyeul.Yoo.mssm.edu>
Date: Tue, 22 Mar 2011 18:26:03 -0400

Dear Amber Users,

I'm trying to use "residuegen" to split my ligand into smaller parts.

I have two questions.

1. "residuegen" requires two input files, xxx.ac and xxx.esp. I could easily get xxx.ac file from pdb file of the ligand.
But I have no idea how to get xxx.esp file with only pdb files.
Should I run any gaussian program to have gout and run "espgen"? Is that the only way to obtain esp files?

2. Can I use only one input file for "residuegen" to split multiple residues from one ligand?
If I want to split my small molecules into 3 parts (let's call them AAA, BBB, CCC), should I have three corresponding input files?
If I can use only one file to split one molecule into smaller residues, how should I specify them using SEP_BOND?

Please let me have your advices

Best regards,

Seungyeul Yoo, Ph.D Candidate
Department of Structural and Chemical Biology
Mount Sinai School of Medicine
Box 1677, 1425 Madison Avenue, New York, NY 10029
East Building, 16th floor, Room 16-34A
New York, NY 10029
+1 (212) 6595477

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Received on Tue Mar 22 2011 - 15:30:03 PDT
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