Dear,
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
autoimage
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
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
Tel:(31)3409-5776
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Received on Wed Aug 30 2017 - 20:30:02 PDT
