AMBER Archive (2005)

Subject: RE: AMBER: strange minimalization output

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Aug 02 2005 - 10:47:59 CDT

> I have just started to work with AMBER so I am quite newbie in it.
> I have some questions to ask.

If you haven't already you should try the tutorials, particularly the
beginning amber workshop ones, on
http://amber.scripps.edu/tutorial/index.html these will answer a lot of your
questions.
 
> I am doing water minimalization of Kinase-ATP complex.
>
> This is my minimalization input:
>
> &cntrl
> imin=1, maxcyc=20000, ncyc=5000,
> scee=2.0,
--^^^^^^^^^^^^
|
You should not mess with the default for this value unless you know what you
are doing. Are you really using a force field earlier than 1994? If not then
this should be the default of 1.2. Using 2.0 will result in incorrect
results.

>cut=9.0

A cut of 8.0 is fine for periodic boundaries.

>, ntb=2, ntp=2,

you probably want to do minimisation with constant volume, ntb=1 but this is
not such a big issue. However, ntp=2 is. You want to use isotropic scaling
(ntp=1) when doing constant pressure simulations unless you really know what
you are doing.

> dielc=70,

This is a default of 1.0 and need only be changed for gas phase simulations.
For periodic simulations with explicit solvent you should leave this at 1.
For a gas phase simulation you would typically set this to 80.0 to simulate
water.

> nsnb=20,
> ntpr=5,
> ibelly=0,
> &end

> not ca
> 0
> FIND
> * * S *
> * * B *
> * * 3 *
> * * E *
> N * M *
> C * M *
> O * M *
> SEARCH
> RES 1 9999
> END
> END

All of the section above is redundant and not needed since you have
specified a restraint force constant of 0. You have also not turned on
restraints in the input file (ntr=1).
 
> How do I know the value of dielc?

It is the relative dielectric constant of the solvent. Check any standard
physics text book. You don't need to change this from the default for
explicit solvent simulations.

> Sometimes Amber stops the calculations with an error:
> "RESTARTED DUE TO LINMIN FAILURE"

This has been discussed many times, search the amber mailing list archive,
paste it into google and/or check the FAQ's on the amber website.

> Why it is happening and what can I do to do minimalization to the
> 20000 steps?

Why do you want to do the minimisation? It will only get you to the nearest
local minimum, you won't learn much from it. You need to do dynamics to move
away from local minima.

Try the tutorials and things will become much clearer.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | 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 ready every day, and should not be used for urgent or sensitive issues.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu