AMBER Archive (2007)

Subject: Re: AMBER: ow to split MDCRD file using ptraj

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Fri Aug 24 2007 - 21:17:27 CDT

Hi,

Look in the 'ptraj' session in the manual. Specifically, you will use
'trajin' and 'trajout'. You can use the options for 'trajin' to only
load some frames, then use 'trajout' to save them to some file.

Good luck,
Gustavo.

On 8/24/07, priya priya <priyaanand_27_at_yahoo.co.in> wrote:
> Dear all,
>
> As per your suggestion i have to split my mdcrd file using ptraj, would you
> please tell me how to do that.
>
> Regards
> Priya
>
> Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> Hi Priya,
>
> If your mdcrd file is larger than 2GB it is very likely that VMD won't read
> it. You can use ptraj to split it up into chunks or alternatively build a
> smaller file with say only every 100th step in it.
>
> Also VMD cannot deal with pathnames longer than a certain number of
> characters - I don;t know the exact number, probably 128 or 256. Either way
> it manifests itself as an "unable to open" message so you may want to check
> the length of your path and try moving it to a shorter directory tree.
>
> Good luck
> Ross
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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> ________________________________
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> priya priya
> Sent: Thursday, August 23, 2007 08:04
> To: amber_at_scripps.edu
> Subject: AMBER: Unable to open MDCRD file using vmd
>
>
> Dear all,
>
> i have run implicit solvent simulations for 30ns,and for output frequency i
> have given ntwx=50, so i have a big mdcrd file, i want to see the folding
> patway of my protein,but i am not able to open my mdcrd file using vmd1.8.3,
> i am using amber9.
> steps to open mdcrd file i followd are
> 1. opened prmtop file using parm7 option and then loaded mdcrd file and
> selected crd option , but it says unable to load molecule, i have seen mdcrd
> file,it seems to be ok,but it is not working,
> may i know where the problem is.
> i have tred to open 100ps mdcrd file using vmd it is working.
>
> Regards
> priya
>
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