AMBER Archive (2009)

Subject: [AMBER] what the value of "Br" bondi radii, and how to modify "fillratio" error message.

From: B (kinor_at_protein.osaka-u.ac.jp)
Date: Thu Dec 17 2009 - 03:59:29 CST

Dear amber users , developers and professor.

This is the first time for ask from Japan.
Nice to meet you.

I am a student and beginner of using Amber10.

The problems happened when I used MM_PBSA followed by Amber Tutorials(http://ambermd.org/tutorials/advanced/tutorial3/).
(( My object is receptor-ligand complex and, ligand has Br atom.))
 
Before I decide to ask here, I checked , readed Mail Reflector, and tryed to understand my errors, but I couldn't.
So, please help me and tell me the solution, concretely.
 
My problems are two.

First is what's the value of "Br" bondi radii.
Second is how to solve and modfify "fillratio".
Following next sentences, please.

<<<First problem >>>.
----------------------------------------------------------------------
I noticed an error message in the mm_pbsa calculations:
 
 Generate PQR
 No radius found for BR
  
 It was pinpointed to be in the mm_pbsa_calceneent.pm, in which the Bondi
 radii for different types of atoms are generated in the molsurf
 calculation:
 
 sub generate_pqr(){
 ###################
 ....
 # Bondi radii + 1.4A and probe radius of 0.0A yields SAS
 # Bondi radii + 0.0A and probe radius of 1.4A yields molecular surface
 # Bondi radii + 0.0A and probe radius of 0.0A yields vdW surface
 my %exp_rad = (
 "N" => 1.550 + 1.400,
 "H" => 1.200 + 1.400,
 "C" => 1.700 + 1.400,
 "O" => 1.500 + 1.400,
 "P" => 1.800 + 1.400,
 "S" => 1.800 + 1.400,
 "FE" => 1.300 + 1.400,
 "Na+" => 1.200 + 1.400,
 "Cl-" => 1.700 + 1.400,
 "MG" => 1.180 + 1.400,
 );
 ....

 However, the parameters for BR not there.

So , by the way of experience,
 I substituted "Br" value, which is vdw radii (= 1.800) , like next sentences,
 "Na+" => 1.200 + 1.400,
 "Cl-" => 1.700 + 1.400,
 "MG" => 1.180 + 1.400,
 "Br1" => 1.800 + 1.400,
 );
 ....
Then, there was not the same message error.
(However , different error message was appearance.
  The different message was written under this section.)

Does my playing wrong?
If it's wong, how to deal with this error message?
What the value of Br's Bondi radii??
------------------------------------------------------------------------------------

<<<<Second question>>>
------------------------------------------------------------------------------------

Keeping substitution of Br's vdw radii (= 1.800) in mm_pbsa_calceneent.pm
, I continued to calcurate binding energy the calculation. (like Amber tutorial: http://ambermd.org/tutorials/advanced/tutorial3/section3.htm)

However , the error was happend , again.

The message is that

/home1/kino/amber10/exe/sander -O -i pbsa_lig.in -o pbsa_lig.1.out -c ./snapshot_lig.crd.1 -p ./ligand.top
not successful

So I tryed to see pbsa_lig.1.out and noticed the error message that

PB Bomb in setgrd(): focusing grid too large 2
                                   reset fillratio to a larger number 2.000
 
I realized I need to change "fillratio"value, but I could not know the location, where fillratio is.
Therefore I confused where do I change the value of fillration.
How to modify fillratio error message??

Please help and teach me concretelly.

----------------------------------------------------

The best regard. Thank you.

Ryohei
at Osaka University Student from Japan.

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