Hello,
I am trying to use Amber to run simulations on a large non-biomacromolecule containing around 14,000 atoms. The molecule is novel, and I have created my own PDB file to run. All atoms are recorded as HETATM, and all located in one residue (also novel) called X5Q. A section of the PDB looks like:
HETATM 1 1 X5Q A 999 62.89 91.22 -31.50 C
HETATM 2 2 X5Q A 999 63.54 91.22 -30.27 N
HETATM 3 3 X5Q A 999 63.31 90.19 -29.35 C
...
...
...
HETATM13678 E178 X5Q A 999 62.09 80.75 -27.21 O
HETATM13679 E179 X5Q A 999 61.38 89.52 -30.68 C
HETATM13680 E180 X5Q A 999 61.70 90.52 -31.57 N
The problem I run into occurs when I attempt to load the file to tleap. The loadpdb command creates a new unit, but any attempt to manipulate it results in an error of : FATAL: Atom (BLANK) does not have a type. This occurs for all atoms.
Any help on this issue would be greatly appreciated.
Thank you,
Clayton
Clayton Buback
Chemical Engineering with a Biochemical Emphasis,
Missouri University of Science & Technology
President, International Society for Pharmaceutical Engineering
Secretary, Scrubs Pre-Health Society
Public Relations Coordinator, International Students Club
Pledge Education Teaching Assistant, Alpha Chi Sigma
cbnf6.mail.mst.edu<mailto:cbnf6.mst.edu>
(314)584-0002
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Received on Thu Sep 06 2012 - 17:30:02 PDT
