Hi
I minimized the 6-aminopurine itself twice.
1) the frcmod (generated by parmchk) was:
remark goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
ca-cc-na-hn 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
h5-na-cc-nd 1.1 180.0 2.0 Using default value
ca-ca-ca-nd 1.1 180.0 2.0 Using default value
ca-nb-ca-nh 1.1 180.0 2.0 Using default value
ca-hn-nh-hn 1.1 180.0 2.0 Using default value
h5-nb-ca-nb 1.1 180.0 2.0 Using default value
ca-na-ca-nb 1.1 180.0 2.0 Using default value
NONBON
Then, I minimized the ligand in vacuum and without periodicity and the molecule was not planar any more.
2) I increased the force constants for improper angles and thus the frcmod file was:
remark goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
ca-cc-na-hn 5.6 180.0 2.0 General improper torsional angle (2 general atom types)
h5-na-cc-nd 5.6 180.0 2.0 Using default value
ca-ca-ca-nd 5.6 180.0 2.0 Using default value
ca-nb-ca-nh 5.6 180.0 2.0 Using default value
ca-hn-nh-hn 5.6 180.0 2.0 Using default value
h5-nb-ca-nb 5.6 180.0 2.0 Using default value
ca-na-ca-nb 5.6 180.0 2.0 Using default value
NONBON
Then I ran a minimization as before and the molecule had a planar conformation. So it look like a problem was solved
Then i got an additional problem:
I created topology and coordinate files for the 6-aminopurine-PknG complex (following the steps of the tutorial B4) and of course i used the ligand's frcmod file manually modified (which worked for the ligand alone).
Then i minimized the complex:
Initial minimisation of PknG-Adenine complex
&cntrl
imin=1,
maxcyc=500,
ncyc=250,
ntb=0,
igb=0,
cut=12
/
After the minimization the 6aminopurine within the binding pocket had lost again is planarity. It had a distorted conformation.
Do you have any idea of how i could avoid the ligand distortion when i minimized the whole complex and not only the ligand itself?
Thank you
Valentina
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: Thursday, April 24, 2014 2:00 PM
To: AMBER Mailing List
Subject: Re: [AMBER] AMBER minimization problem
On Thu, Apr 24, 2014, Valentina Romano wrote:
>
> When i say 'the ligand lost its planarity' i mean that the molecule
> which is a planar aromatic molecule is not planar anymore after the
> minimization and this is strange.
But you don't say whether the deviation from planarity is large or small.
Small deviations from planarity are very common (e.g. in purines), and are
likely to be found in aromatic rings that are ligands in proteins as well.
>
> I'll try to minimaze the ligand itself without the protein and see what
> appends.
OK...good....dac
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Received on Thu Apr 24 2014 - 07:00:03 PDT
