Re: [AMBER] ATP minimization

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Mon, 27 Feb 2012 09:22:15 +0100

Dear Sangita Kachhap,

> I have not able run this command
>
> Shall I use link you have given in command line:
> xleap -f
> http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff

I ask you to excuse me; presenting this command was a bad idea...
This is just a project ;-)

> or I have to run command:
> xleap -f script1.ff

Yes this is the command you have to run...

> I have tried both fist one didnt run
>
> When try second, Its showing
>
>> POP = loadmol2 ./tripos1.mol2
> Could not open file ./tripos1.mol2: No such file or directory

Read the file script1.ff and you will see the following commands:

########## Activate the 89 lines below: perl -p -i.old -e
's/\#\#\!\# //g' script1.ff
########## Remove the 89 lines below: grep -v "to be replaced by the
correct tripos" script1.ff > script1-new.ff

these two commands have to be executed so that the mol2 file names
generated by R.E.D. corresponds to these stored in R.E.DD.B.

then xleap -f script1-new.ff

regards, Francois



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Received on Mon Feb 27 2012 - 00:30:02 PST
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