AMBER Archive (2007)

Subject: AMBER: ow to split MDCRD file using ptraj

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Fri Aug 24 2007 - 02:34:27 CDT


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 |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.
  

       
---------------------------------
   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
      

---------------------------------
   Why delete messages? Unlimited storage is just a click away.

       
---------------------------------
 5, 50, 500, 5000 - Store N number of mails in your inbox. Click here.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu