Hi Catherine,
You can load a pdb file without water and Na+ into VMD before loading the
mdcrd - the pdb file you can make using ptraj if you like.
Alternatively, go back to tleap/sleap/xleap and write a prmtop without
water and Na+ and use that.
--Marc
On 8 March 2012 15:47, Catein Catherine <askamber23.hotmail.com> wrote:
>
> Dear Sir,
>
> I have a large number of mdcrd files. I need to view and analysis all
> these files in one goes with VMD. However, due to the memory reason, I
> cannot load all these files to VMD.
>
> Could you mind to suggest how to use ptraj to convert all these files to a
> format that readable in VMD with less memory.
>
> I think of using ptraj to convert all these mdcrd files to single mdcrd
> without water and Na+. However, after doing it, the inonegoes.mdcrd is
> reduced by ten times. But I cannot read this file with VMD using my
> original *.prmtop (after or after adding water or Na+) anymore. How to do
> it properly? Please help.
>
> trajin ../1.mdcrd.gz
> trajin ../2.mdcrd.gz
> trajin ../3.mdcrd.gz
> trajin ../4.mdcrd.gz
> trajin ../5.mdcrd.gz
> trajin ../6.mdcrd.gz
> trajin ../7.mdcrd.gz
> strip :WAT
> strip :Na+
> trajout inonegoes.mdcrd nobox
>
>
>
>
>
>
>
>
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Received on Thu Mar 08 2012 - 08:00:04 PST
