AMBER Archive (2008)

Subject: RE: AMBER: drawing repeated units

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jun 24 2008 - 16:40:26 CDT

Hi Taufik,

Yes you will have to manually specify the parameters for the additional
bonds / angles and dihedrals. The standard way to do this would be to
include them in a frcmod file, either as a standalone file or as part of the
file produced by parmchk when you built the original units in antechamber.
The actual parameters you use is somewhat of a research question.

As a starting point you could create a capped version of the two units
bonded together and run this through antechamber and then parmchk so that it
gives you additional parameters for the bond between residues, you could
then cut and paste these into the main frcmod file you are using - I.e.
discard all the charges, mol2/prep files etc from this antechamber step and
just use it as a short circuit way of getting "guesstimates" of the
parameters for the intervening bonds.

I hope this helps,
All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Taufik Al-Sarraj
> Sent: Tuesday, June 24, 2008 3:16 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: drawing repeated units
>
> Hi,
>
> I tried this few times and it works up to saveamberparm. the error i get
> is could not find angle parameter: etc etc
> and No torson terms for ....
> i built the units properly (using antechamber) but when two units are
> connected a new bond is created along with new angles and torsions, how
> can describe those? should i set them manually?
>
> I know the mol = sequence { FPR REPU REPU REPU REPU ENDU} is working
> because when i type edit mol i see the chain as expected.
>
> I am using amber9 and i usually use xleap -s -f leaprc.ff99SB
>
> Thanks,
> 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 |
> >
> > 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.
> >
> >
> >
> >
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