AMBER Archive (2005)

Subject: AMBER: How to make PDB file by myself

From: Mayumi Haga (haga_at_cir.tohoku.ac.jp)
Date: Mon Jan 24 2005 - 22:23:32 CST

Dear Sirs.

I am using amber7and 8,
I want to ask you about how to make PDB format file of HOPG(graphite)
substrate. It consists only of carbon, so the amount of C atoms has got
huge.

I made PDB format file by using Gauss View, there are about 8000atoms. I
tried to read this PDB format file by XLEaP, successed to read atoms with
many errors, but these atoms were not connected.

I tried to make PDB format file by Chem3D, though it contains binding
infomation, XLEaP could only read untill 1000 carbon atoms.

I couldn't find how to read large amount of C atoms by XLEaP. untill 1000
atoms, it could read by using C1-C999 as a atom name. and atom type CT . But
I couldn't read over 1000 atoms. Should I change residue number or residue
name?

I want to know how to make PDB format files like artificial substrate by
myself.

Sincerely yours
 
Mayumi

******************************************************************
Mayumi Haga

Kawano Laboratory, Center for Interdiscipinary Research,
Tohoku University, Japan
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