[AMBER] convert .mae topology to .prmtop topology?

From: Marcelo Andrade Chagas <andrade.mchagas.gmail.com>
Date: Thu, 31 Aug 2017 00:14:56 -0300


I'm trying to use cpptraj to do a clustering

However, the simulations were done with NAMD

So I have topology files (.mae) and trajectory files (.dcd)

I'm trying to use the following:

cpptraj -p <topology> -y <input dcd> -x output.mdcrd

Or the file:

parm topo.prmtop
trajin CLN025-0-protein-000.dcd
strip :WAT
strip :Na+
strip :Cl-
trajout mol.mdcrd netcdf

The problem I'm noticing is with the topology file,

And I believe that the way we try to convert .mae to .prmtop is wrong

How to do this?

How to convert .mae topology to .prmtop topology?

Best regards


Marcelo Andrade Chagas, MSc
(PhD student)
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
* http://lqcmm.qui.ufmg.br/
Departamento de Química da Universidade Federal de Minas Gerais - UFMG
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Received on Wed Aug 30 2017 - 20:30:02 PDT
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