AMBER Archive (2006)

Subject: AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap

From: Lwin, ThuZar (ThuZar.Lwin_at_stjude.org)
Date: Tue Jul 25 2006 - 19:39:32 CDT

Hi amber community,

 

I am learning how to do thermodynamic integration using amber8. I would
like to mutate Alanine to Glycine by mutating the side chain CH3 to H.
Here is what I did in tleap. Please let me know what I am doing wrong.

 

Thank you

 

a = sequence{ALA}

 

set a pert true

set a.CB pertName HA3

set a.CB pertType H1

set a.CB pertCharge 0.000

 

set a.HB1 pertName DUMM

set a.HB1 pertType DU

set a.HB1 pertCharge 0.000

 

set a.HB2 pertName DUMM

set a.HB2 pertType DU

set a.HB2 pertCharge 0.000

 

set a.HB3 pertName DUMM

set a.HB3 pertType DU

set a.HB3 pertCharge 0.000

 

saveAmberParmPert a ala_p.parm ala_p.rst

 

And the leap.log file produced the following message.

 

> set a.CB pertCharge 0.000

a.CB: not a container (e.g. residue)

usage: set <container> <parameter> <object>

   or: set default <parameter> <value>

>

> set a.HB1 pertName DUMM

a.HB1: not a container (e.g. residue)

usage: set <container> <parameter> <object>

   or: set default <parameter> <value>

> set a.HB1 pertType DU

a.HB1: not a container (e.g. residue)

usage: set <container> <parameter> <object>

   or: set default <parameter> <value>

> set a.HB1 pertCharge 0.000

a.HB1: not a container (e.g. residue)

usage: set <container> <parameter> <object>

   or: set default <parameter> <value>

>

> set a.HB2 pertName DUMM

a.HB2: not a container (e.g. residue)

usage: set <container> <parameter> <object>

   or: set default <parameter> <value>

> set a.HB2 pertType DU

a.HB2: not a container (e.g. residue)

usage: set <container> <parameter> <object>

   or: set default <parameter> <value>

> set a.HB2 pertCharge 0.000

a.HB2: not a container (e.g. residue)

usage: set <container> <parameter> <object>

   or: set default <parameter> <value>

>

> set a.HB3 pertName DUMM

a.HB3: not a container (e.g. residue)

usage: set <container> <parameter> <object>

   or: set default <parameter> <value>

> set a.HB3 pertType DU

a.HB3: not a container (e.g. residue)

usage: set <container> <parameter> <object>

   or: set default <parameter> <value>

> set a.HB3 pertCharge 0.000

a.HB3: not a container (e.g. residue)

usage: set <container> <parameter> <object>

   or: set default <parameter> <value>

>

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