AMBER Archive (2008)

Subject: Re: AMBER: using packmol file in Amber

From: oguz gurbulak (gurbulakoguz_at_yahoo.com)
Date: Thu Dec 04 2008 - 09:36:03 CST

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_at_biomaps.rutgers.edu> wrote:
From: David A. Case <case_at_biomaps.rutgers.edu>
Subject: Re: AMBER: using packmol file in Amber
To: amber_at_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_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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu

      

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu