AMBER Archive (2006)

Subject: Re: AMBER: pdb error

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Aug 01 2006 - 14:23:30 CDT

Dear Aytug,

It is actually very easy to create the .prmtop files for a system using
leap. The error u are getting says that leap does not recognize some of
the residues in your .pdb file. U have to be sure that leap will
understand what kind of residues you have in your system. Good luck,

Best,

On Tue, 1 Aug 2006, AYTUG TUNCEL wrote:

> hi all,
>
> I am trying to use MM-PBSA method to calculate free energies for my system. the problem is that I have simulated my system using NAMD and now ı have to convert .dcd (NAMD trajectory file) and .pdb (prepared with VMD) to AMBER formats. I guess I have handled the trajectory formats but I also need .prmtop file for my system. When I try to prepare it using LeAP it gives the error;
>
> "unknown residue: TIP number xxx type: Nonterminal"
>
> Is there any way to convert VMD prepared PDB format to the AMBER format so that LeAP can recognize it.
>
> Thanks for any help.
>
> Aytug TuncelÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿR
>
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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
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