AMBER Archive (2007)

Subject: AMBER: "FATAL: Atom xxx does not have a type."

From: Fred Baba (fred.baba_at_gmail.com)
Date: Tue Jun 26 2007 - 12:59:51 CDT

Hello,

I'm attempting to prepare files for energy minimization in Sander, but
I'm unable to make the .prmtop and .inpcrd files. The systems in
question are apparently too large to create frcmod parameters in
antechamber. I start leap with the following commands:

xleap -s -f leaprc.ff99 # '99 Force field data
source leaprc.gaff # and GAFF data, right?
UN2 = loadpdb "10gs_protein.pdb"
loadamberprep 10gs_protein.prepin
# Can only make the prep file with Leap. AC crashes due to system size
saveamberparm UN2 10gs_protein.prmtop 10gs_protein.inpcrd

Leap then lists H all the added, claiming that they do not have a type, i.e.
FATAL .R<LYS 416>.A<HE1 26> does not have a type. What would be
causing this error. I came across it before but the use of force field
parameters(frcmod) got rid of the error, so I didn't worry about it.
Any help would be greatly appreciated.
Cheers,

Fred Baba 

-- 
Frederick Baba
Massachusetts Institute of Technology
Class of 2010
Biological Engineering || Computer Science
Email: fredbaba_at_mit.edu, fred.baba_at_gmail.com
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