AMBER Archive (2009)

Subject: RE: [AMBER] Error in trajin and rms

From: Pansy Patel (pdpatel_at_mail.ucf.edu)
Date: Thu Apr 02 2009 - 14:25:58 CDT

Thanks

Pansy

>>> iccy liu <hbliu92_at_hotmail.com> 4/2/2009 3:19 PM >>>

Hi,

The program is ptraj.

In your case, You could put all your commands in a file, name it
"polyAT_vac_md1_12Acut.calc_rms", then run
ptraj polyAT_vac.prmtop < polyAT_vac_md1_12Acut.calc_rms

Iccy

> Date: Thu, 2 Apr 2009 14:58:47 -0400
> From: pdpatel_at_mail.ucf.edu
> To: amber_at_ambermd.org
> Subject: [AMBER] Error in trajin and rms
>
> Hello
>
> I am trying to run the tutorial b1 section 3
> The Md runs successfully with both vacuum and implicit solvent
>
> However, when I typed the commands to run trajectory the following
error messages appeared,
> I can find the ptraj file in the exe directory, but not trajin and
rms.
>
> [PATH]$ trajin polyAT_vac_md1_12Acut.mdcrd
> bash: trajin: command not found
>
> [PATH$ rms first mass out polyAT_vac_md1_12Acut.rms time 0.1
> bash: rms: command not found
>
> [PATH]$ ptraj polyAT_vac.prmtop < polyAT_vac_md1_12Acut.calc_rms
> bash: polyAT_vac_md1_12Acut.calc_rms: No such file or directory
>
> Can somebody tell me what I am doing wrong?
>
> Best regards,
>
> Pansy D Patel
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_________________________________________________________________
Drag n’ drop—Get easy photo sharing with Windows Live™ Photos.

http://www.microsoft.com/windows/windowslive/products/photos.aspx_______________________________________________

AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber