Re: [AMBER] "Spiderweb"

From: FyD <>
Date: Thu, 26 Apr 2012 17:57:31 +0200

Dear Min,

> i successfully create the PRMTOP file and INPCRD file succesfully
> based on tutorial but on my own ligand without error but when i load
> the PRMTOP and INPCRD into the VMD my molecules become "spiderweb".
> Will the different theory of charge derivation will yield bonding
> information?

Loading prmtop & prmcrd files in VMD is simple when one has understood
the principle. There are two formats of prmtop files (the last one is
that of Amber7 & after...; I guess the one your use i.e. Amber7 Parm).
Then, you have three different formats for the Amber coordinates. A
first approach is to test all the possibilities & see which one works
- one should work and give you a presentable molecule ;-)

You must load in the order (i) the prmtop file and (ii) the prmcrd
file as a _single_ molecule (like two layers for the given molecule).

Charge derivation will lead to charge values, while the molecular
topology is represented by the atom connectivities defined in the
force field library you use.

You might look at tutorials . the R.E.D.
program uses the P2N file format as input (the molecular topology is
represented by the atom connectivities: i.e. the 'CONECT' keyword) and
generates the mol2 file format as main output with derived RESP or ESP
charge values (in the .<TRIPOS>ATOM section) and molecular topology
(in the .<TRIPOS>BOND section).


regards, Francois

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Received on Thu Apr 26 2012 - 09:00:03 PDT
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