Hi,
Are you receiving an error message? Does the .mae file mean "Maestro"
file format? I'm not sure how you are converting it now so I can't
comment on that, but a brief google search seems to indicate that it's
possible to get a PDB from the Maestro format. If so, you can just use
that as your topology, esp. if all you want to do is clustering.
-Dan
PS - 'strip :WAT,Na+,Cl-' will be more efficient than having 3 'strip' commands.
On Wed, Aug 30, 2017 at 11:14 PM, Marcelo Andrade Chagas
<andrade.mchagas.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Aug 31 2017 - 06:30:04 PDT
