AMBER: pdb error

From: AYTUG TUNCEL <ATUNCEL.ku.edu.tr>
Date: Tue, 01 Aug 2006 22:36:39 +0300

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 ─▒ 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 Tuncel                                                                                                                                       R

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Received on Wed Aug 02 2006 - 06:07:14 PDT
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