AMBER Archive (2009)

Subject: [AMBER] FW: About Amber10 installation "Possible Failure"

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu May 28 2009 - 09:06:31 CDT

From: Navanath Kumbhar [mailto:nmk.biotechnology_at_gmail.com]
Sent: Thursday, May 28, 2009 4:59 AM
To: Ross Walker
Subject: Re: About Amber10 installation "Possible Failure"

 

Dear Sir,

 

i saw the TEST_FAILURE.diff which looks as like

 

possible FAILURE: check gcg.dip.o.dif
/root/Desktop/Amber10/amber10/test/rdc/root/Desktop/Amber10/amber10/test/rdc
352c352
< 196 H5'1 DA 7 0.14 0.62 0.96 

---
>       196 H5'1 DA  7   0.14  0.63      0.96
377c377
<       512 H5'1 DA 17   0.13  0.62      0.98
---
>       512 H5'1 DA 17    0.13 0.63      0.98
---------------------------------------
possible FAILURE:  check stem.dip.o.dif
/root/Desktop/Amber10/amber10/test/pcsa
---------------------------------------
possible FAILURE:  check output_addles.dif
/root/Desktop/Amber10/amber10/test/LES
---------------------------------------
possible FAILURE:  check LES.prmtop.dif
/root/Desktop/Amber10/amber10/test/LES
---------------------------------------
possible FAILURE:  check addles.out.dif
/root/Desktop/Amber10/amber10/test/PIMD/part_pimd_water
---------------------------------------
possible FAILURE:  check addles.out.dif
/root/Desktop/Amber10/amber10/test/ti_mass/pent_LES_PIMD
---------------------------------------
possible FAILURE:  check amoeba_jac.mdout.dif
/root/Desktop/Amber10/amber10/test/amoeba_jac

With reference to Amber manual i gone through this path
/root/Desktop/Amber10/amber10/test/rdc

and see in the:- check gcg.dip.o.dif files from this directory.but there is
same number present as like that of TEST_FAILURE.diff files. So i donot
understand what is the problem.

 

 One thing another is, after writing basic examles( editing pdb
file,topological parameter for give examlpes)  and save as prmcrd as file
name in leap from path given below 

/root/Desktop/Amber10/amber10/src/leap 

 After that i run commands 'Running Minimization for BPTI'

 error is -bash:Running command is not found.

 

I running this commands even after the occurence of POSSIBLE FAILURE
problems. So please tell me whether i going in rihgt direction or not.

 If not please suggest me from which tleap the basic examples run.

 

Thank you.

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