Hello All,
I am planning to do a simulation of prot-CNT (Carbon-Nano-Tube) using Amber.
I checked the structure of CNT, and set all the atoms as CA atom type (from
parm99.dat) in my PDB file.
When I started to prepare the top file using leaprc.ff99SB , Leap denies to
create the top and the message is as follows:
> CNT=loadpdb prot-CNT.pdb
Loading PDB file: ./prot-CNT.pdb
-- residue 179: duplicate [ CA] atoms (total 66)
Warning: Atom names in each residue should be unique.
(Same-name atoms are handled by using the first
occurrence and by ignoring the rest.
Frequently duplicate atom names stem from alternate
conformations in the PDB file.)
Unknown residue: MOL number: 178 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Added missing heavy atom: .R<MET 145>.A<CG 8>
Creating new UNIT for residue: MOL sequence: 179
Created a new atom named: CA within residue: .R<MOL 179>
total atoms in file: 1605
Leap added 1619 missing atoms according to residue templates:
1 Heavy
1618 H / lone pairs
The file contained 1 atoms not in residue templates
FATAL: Atom .R<MOL 179>.A<CA 1> does not have a type.
Can anyone please help me out here, how to set the parameter for CNTs ?
Thank you
Jagur
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Received on Thu Mar 31 2011 - 16:30:02 PDT
