AMBER Archive (2008)

Subject: Re: AMBER: drawing repeated units

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Wed Jun 04 2008 - 15:17:57 CDT

Using a 5 unit process works great. However,

for all my units FPRT, REPU and ENDU i used antechamber to create the
input files.

when i create FIVE = sequence { REPU ... REPU } 5 times, i get the right
sequence even though some atoms are too close together. using EDIT
RELAX from xleap is creating bonds where there should not be any. i also
get new angles/torsions that are not recognized.

I can save the FIVE in pdb format not mol2 and use antechamber to create
the proper prepin files, but i am hoping there is a faster way. same as
in this tutorial
http://www.ambermd.org/tutorials/advanced/tutorial1_adv/index.htm can i
use impose or a file.frcmod. the same way Ross was able to create his
plc.frcmod. Unless Ross used antechamber to create plc.frcmod and then i
have to use antechamber every time there is an unrecognized variable.

Best,
Taufik

Ross Walker wrote:
> Hi Taufi,
>
>> Thank you Ross,
>> It worked!
>> Where can i learn to create a simple leaprc file. is it in any of the
>> tutorials?
>
> A leaprc file is just a text file containing the commands exactly as you
> would enter them in leap. E.g. one could be:
>
> source leaprc.ff99SB
> loadamberparams my.frcmod
> loadoff foo.lib
> loadoff bar.lib
> mol = sequence { FOO BAR FOO BAR }
> saveamberparm mol prmtop inpcrd
> quit
>
> Then you could just run this as:
>
> tleap -s -f my.leaprc
>
> and it would just run those commands and quit.
>
> You can also do:
>
> source my.leaprc
>
> to read it from within an active leap session.
>
>> i can also type mymol = sequence { FPRT REPU ... 50 100 150 and 200
>> times.. ENDU } if writing a one -long- line script is too difficult.
>
> You can't do that in leap unfortunately but you could either write a simple
> perl or shell script that writes leaprc files for you - i.e. writes those
> long lines for you. Or you could build some bigger units. I.e. build a unit
> of 10 REPU's - so you would only have to put 10 of these units in to get a
> 100 repeat.
>
> Good luck,
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | 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 |
>
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