AMBER Archive (2006)

Subject: AMBER: question about building molecules

From: Rita Cassia (
Date: Sun Oct 08 2006 - 06:05:59 CDT


I´m looking for some advice with regard to using AMBER /Antechamber with xleap.

I had tried to build up a complex with 8 Porphyrine (Pheophorbide a) in a "bridge with N, C and H" that could support all 8. I had done that with xleap, using the command sequence. Before connecting them , I had loaded lib files, frcmod files for each Pheophorbide (just once) and the files for the bridge.

The first 4 Pheophorbides caused no problem but when I connected 6 and then 8, xleap had indicated that the distance between 2 pheophorbides were too small. But, nevertheless, the programm has created the lib file, the topology and the coordinate files.

I had taken a look with VMD how those structures look like and I had seen that 2 Pheophorbides were crossing each other.

Unfortunately, when I used NAMD to start my simulation with 0° K, NAMD stopped the simulation, saying that a certain atom was moving too fast and as consequence other atoms too...

It has happened with 5,6 and 8 Pheophorbides.

Looking at the user guide, I had seen a command "impose", that somebody could set a distance between atoms.

My question is: is there a command that I can use after using the command "sequence", that forces all 8 Pheophorbides to keep a distance that cannot bring problems to a simulation?

I would be very, very glad if somebody could share his or her ideas and experiences about this topic with me.

Thanks in advance,

Rita Leite

Institut für Physik
Humboldt Universität zu Berlin

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