Quoting AYTUG TUNCEL <ATUNCEL.ku.edu.tr>:
> Thanks Holger,
>
> I used the command "set default pbradii parse", but it gave me the
> following message,
>
> gbparm value must be 'bondi', 'amber6', 'mbondi', 'pbamber', or 'mbondi2'
> usage: set <container> <parameter> <object>
> or: set default <parameter> <value>
>
> Is there something I am missing? Thanks in advance.
You are right - the 'parse' option didn't make it to the final release
version I just see.
If you are willing to change some of the leap code, here is what is
needed. Goto $AMBERHOME/src/leap/src/leap, then
- edit commands.c such that it looks like (around row 2600)
>>>>>
} else if ( !strcmp( sString, "mbondi2" ) ) {
GDefaults.iGBparm = 6;
VP0(("Using H(N)-modified Bondi radii\n"));
} else if ( !strcmp( sString, "parse" ) ) {
GDefaults.iGBparm = 7;
VP0(("Using PARSE radii\n"));
} else {
VP0(("gbparm value must be 'bondi', 'amber6',
'mbondi', 'pbamber', 'mbondi2' or 'parse'\n"
setUsage();
}
<<<<<
- edit unitio.c such that it looks like (around row 5228)
>>>>>
} else if ( GDefaults.iGBparm == 3 ){ /* radii from
Huo & Kollman */
switch( iElement ){
case 1: dGBrad = 1.15; break;
case 6: dGBrad = 1.85; break;
case 7: dGBrad = 1.64; break;
case 8: dGBrad = 1.53; break;
case 9: dGBrad = 1.53; break;
case 15: dGBrad = 2.02; break;
case 16: dGBrad = 2.00; break;
case 17: dGBrad = 1.97; break;
case 35: dGBrad = 2.03; break;
case 53: dGBrad = 2.10; break;
default: dGBrad = 1.5; break; /* DAC
made this up! */
}
} else if ( GDefaults.iGBparm == 7 ){ /* PARSE radii */
switch( iElement ){
case 1: dGBrad = 1.00; break;
case 6: dGBrad = 1.70; break;
case 7: dGBrad = 1.50; break;
case 8: dGBrad = 1.40; break;
case 15: dGBrad = 2.00; break;
case 16: dGBrad = 1.85; break;
default: dGBrad = 1.50; break; /* DAC
made this up */
}
}
FortranWriteDouble(dGBrad);
<<<<<
Recompile leap, then generate a new parmtop file with "set default
pbradii parse" . You might want to check the "FLAG RADII" section in
this parmtop file to make sure that the proper PARSE radii are written
there.
Best regards
Holger
>
> Aytug
>
>
>
> -----Original Message-----
> From: Holger Gohlke <gohlke.bioinformatik.uni-frankfurt.de>
> To: amber.scripps.edu
> Date: Wed, 4 Apr 2007 11:24:17 +0200
> Subject: Re: AMBER: parse radii
>
> Am Mittwoch, 4. April 2007 11:10 schrieb AYTUG TUNCEL:
>> Hi all,
>>
>> Is it possible to use parse radii in mm_pbsa calculations without Delphi in
>> Amber8 ? Thanks in advance.
>
> Yes, you can do so by generating a prmtop file via leap using the
> "set default
> pbradii parse" option and running mm_pbsa with the pbsa module (PROC=2),
> setting RADIOPT=0 and using this prmtop file. Make sure the SURFTEN/SURFOFF
> values and PRBRAD are according to what they should be when using the PARSE
> radii.
>
> Best regards
>
> Holger
>
>>
>> Aytug
>>
>> -----------------------------------------------------------------------
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>
> --
> ++++++++++++++++++++++++++++++++++++++++++++++++++
> Dr. Holger Gohlke
> Juniorprofessor fuer Molekulare Bioinformatik
>
> J.W. Goethe-Universitaet
> Fachbereich Biowissenschaften
> Institut für Zellbiologie und Neurowissenschaft
> Max-von-Laue-Str. 9
> 60438 Frankfurt/Main
> Germany
>
> Tel.: (+49) 69-798-29411; Fax: (+49) 69-798-29527
> Email: gohlke.bioinformatik.uni-frankfurt.de
> URL: http://www.uni-frankfurt.de/~hgohlke
> ++++++++++++++++++++++++++++++++++++++++++++++++++
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
>
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Received on Wed Apr 11 2007 - 06:07:18 PDT
