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