[AMBER] parameter for CNTs

From: Jagur Lambix <jagurlambix.yahoo.com>
Date: Thu, 31 Mar 2011 16:02:14 -0700 (PDT)

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

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Received on Thu Mar 31 2011 - 16:30:02 PDT
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