AMBER Archive (2007)

Subject: Re: AMBER: Saving (.)prepin file

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 10 2007 - 12:45:58 CDT

On Mon, Jul 09, 2007, Johnson Agbo wrote:
>
> My problem is still not resolved. I used antechamber to create the file
> bz.prepin as shown below
>
> 0 0 2
>
> This is a remark line
> molecule.res
> 1 INT 0
  ^^^^

The system thinks your residue is named "1" I think you can use the -rn
option to antechamber to get the name you want. My recommendation is to
use the mol2 format as output, rather than prepin: we are trying to retire
the prepin format, which is nonstandard and has lots of quirks.

>
> The commands given out are as follows:
> tleap
> source leaprc.ff99
> BZ=loadAmberPrep bz.prepin

This is the wrong syntax. You can type "help loadAmberPrep" at the tleap
command line to see what is correct.

>
> I think I now have a unit called BZ, but on typing list, all I found is
>
> 1 ACE ALA ARG ASH ASN ASP
 ^^^^^

As above, "BZ" does not exist in the list, but "1" does.

...hope this helps....dac

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