AMBER Archive (2007)

Subject: RE: AMBER: Attaching capping groups

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Apr 15 2007 - 22:49:26 CDT

Dear Neelanjana,
 
It is normal to get very 'bad' geometries when using leaps sequence command
since it literally just appends the units together without any
considerations for steric clashes etc. However, the extremely long bond to
one of the hydrogens seems a bit odd. You might want to try using leap's
relax command. In xleap edit the complete unit highlight parts of the system
and then select relax selection (under the edit menu I think but don't quote
me on this). This should hopefully clean up the structure enough that you
can then successfully minimize and run MD in sander.
 
For the second part of your question this depends on what the organic groups
are on the ends. If they are ACE or NME and everything else is standard
amino acids you should be fine. However, if the capping groups are not amino
acids then you will need to provide parameters for them. The simplest
solution here is to use antechamber and the gaff force field. See the
tutorials on the amber site for an example of using antechamber... I believe
antechamber was available in amber 7. If not you can download an updated
standalone version from:
http://amber.scripps.edu/antechamber/antechamber.html
 
All the best
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> | PGP Key
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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Neelanjana Sengupta
Sent: Thursday, April 12, 2007 19:55
To: amber_at_scripps.edu
Subject: Re: AMBER: Attaching capping groups

Dear Ross,

Thanks. This worked, producing the correct atoms. The coordinates of the
methyl hydrogens are, however, quite odd (see attached pdf for picture), but
it should work out during minimization. I just wanted to ask if this is
normal.... I am using amber7.

I did not use any initial coordinates for this case. I will soon be
simulating some artificial peptides which are capped at both ends by organic
groups, for which I have coordinates (as pdb files). Will I need to modify
the leaprc file? I would be very grateful if you could point out the steps
required to do this.

Regards,
Neelanjana

On 4/11/07, Ross Walker <ross_at_rosswalker.co.uk> wrote:

Dear Neelanjana,
 
$AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
 
mol = sequence { ACE ALA NME }
saveamberparm mol prmtop inpcrd
 
will accomplish what you want to do.
 
Good luck...
Ross

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.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.

 

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Neelanjana Sengupta
Sent: Wednesday, April 11, 2007 18:29
To: amber_at_scripps.edu
Subject: AMBER: Attaching capping groups

Hi,

I want to create alanine dipeptide by including the capping groups ACE and
CTE (see below) to the N-terminus and C-terminus of alanine. Do I need to
modify the leaprc file for this?
I am using amber7. I could not identify suitable terminal groups in the
all_aminoct94.lib and all_aminont94.lib.
Some advice is greatly appreciated.

'ACE' is (C=O)-(CH3)
'CTE' is (CH3)-(NH)

Thanks, 

-- 
****************************************
Neelanjana Sengupta, PhD student
Dept. of Chemistry 
Univ. of California-Irvine
Irvine, CA 92697
USA
Phone: 1-949-824 9921
email: sengupta_at_uci.edu
**************************************** 

-- 
****************************************
Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
USA
Phone: 1-949-824 9921 
email: sengupta_at_uci.edu
**************************************** 

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