AMBER Archive (2009)

Subject: RE: [AMBER] The PDB file was not recognized by Amber, what can i do?

From: Ross Walker (
Date: Tue Apr 28 2009 - 22:56:27 CDT

Dear Houyang,

> Can you tell me more detail about "made the parametrisation with
> gaussian
> calculations and antechamber"?
> Besides, which tutorials can show me more details?
> By the way, i attached pdb file which i am able to load it in VMD.

The fact that you can load it into VMD does not mean anything about whether
you can actually use it for a classical MD simulation. You need to realize
here that you require atom types, connectivity, parameters, charges etc for
a classical simulation which simply do not exist in the default libraries.
These you will need to provide. Since you do not appear to have realized
this I would advise you to consult some text books on molecular mechanics
and molecular dynamics to make sure you are fluent with the underlying
theory before you proceed further.

With respect to tutorials I would suggest working through the following from
the amber website:

This will not tell you exactly what to do but will hopefully get you
thinking on the correct path for what information is needed / how to proceed

With reference to your pdb file:

ATOM 1 C C A 1 3.887 0.000 0.000 1.00 0.00
ATOM 2 C C A 1 3.697 1.201 2.115 1.00 0.00
ATOM 3 C C A 1 3.887 0.000 1.410 1.00 0.00

This is not a valid pdb format file. Firstly for a given residue all atom
names need to be unique. Thus you need to rename your carbons to be C1, C2,
C3 etc. I would also suggest making the residue name 3 letters long instead
of just C. Then you need to build a library file for your carbon nanotube
that defines what all the atom types, charges and parameters are. For
parameters I would suggest that you consult the literature to see what
people have tried before.

AMBER was designed originally for simulations of proteins. Thus what you are
trying to do, while fairly easy to do, is outside of the original design
specs and thus you will need to be prepared to do some work yourself to get
it working.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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