AMBER: How to make PDB file by myself

From: Mayumi Haga <>
Date: Tue, 25 Jan 2005 13:23:32 +0900

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

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

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

Sincerely yours

Mayumi Haga

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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Tue Jan 25 2005 - 04:53:00 PST
Custom Search