I created a lib file and loaded it into leap . And also I generated a packmol pdb file and added TER cards into the packmol pdb file. But after I load packmol pdb file to leap , same errors and warnings happened. I attached the packmol pdb file. Could you please help me about this problem?
Thanks in advance
--- On Tue, 12/2/08, David A. Case <case.biomaps.rutgers.edu> wrote:
From: David A. Case <case.biomaps.rutgers.edu>
Subject: Re: AMBER: using packmol file in Amber
To: amber.scripps.edu
Date: Tuesday, December 2, 2008, 8:19 AM
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.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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Received on Fri Dec 05 2008 - 18:44:04 PST
