AMBER Archive (2008)

Subject: Re: AMBER: using packmol file in Amber

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Dec 02 2008 - 08:19:20 CST

On Tue, Dec 02, 2008, oguz gurbulak wrote:

> check OAS ( I got some errors and warnings )

> I created a residue 'HEP' but I didn't save it as a lib file so I
> didn't load a lib file into leap.

If I assume(?) that your error message was something like this:

> > FATAL: Atom .R< HEP 1>.A<C1 1> does not have a type.

then the fact that you didn't load the HEP library into leap would explain
this error message.

> And also I couldn't send a mail
> includes my packmol pdb file to amber_at_scripps.edu.

That is because the attachment was way too large for the mail server. I have
emailed you about this earlier.

> The packmol pdb file I created does
> not have TER cards betwen each separate molecules.

That is bad..among other things, you will have to fix this.

Suggestion: start small, and work one step at a time. Be sure that you can
read and process a single HEP structure. Then use packmol to create a small
number, and try that. Then you can try to work with a very large number of
molecules.

...dac

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