Jason thanks a lot again !
This is really incredible service ! No way to move from Amber :))
What is still not so clear is the easest way how to incorporate scee = 1.2
into
nmode calculation.
I succeeded with this method which doesn.t require changing C/F sources
/recompiling of Amber:
I just "hacked" file
mm_pbsa_createinput.pm
by adding line:
print OUT " scee= 1.2,\n";
to relevant block:
$name = "nmode" . $suf . ".in";
open(OUT,">$name") || die(" $name not opened\n For details see:
$HTMLPATH#create_nmode_nmodein_not_opened\n");
print OUT "File generated by mm_pbsa.pl\n";
print OUT " &data\n";
print OUT " ntx = 0,\n"; # Binary format is no longer supported
print OUT " ntrun = 1, nvect = $nvect,\n";
print OUT " drms = $nmdrms,\n";
print OUT " dielc = 4.0, idiel = 0,\n";
print OUT " idecomp= $idecomp,\n";
print OUT " scee= 1.2,\n";
print OUT " &end\n";
print OUT "END\n";
close(OUT);
however especially for those who have not so easy possibility to change
Amber files (i.g. users of supercomputer centers ... ) might be useful
some another way with no necessity to change Amber sources.
So is it possible:
a)
to run mm_pbsa.pl using "by hand" created sandmin*.in nmode*.in files
instead regular mm_pbsa.in file ?
With regular input file, the syntax to run MMPBSA calculation is:
mm_pbsa.pl mm_pbsa.in > mm_pbsa.out
So using sandmin*.in nmode*.in should be similar to:
mm_pbsa.pl sandmin*.in nmode*.in > mm_pbsa.out
but if using exactly this form it doesn.t work.
b)
Another possibility might be to start mm_pbsa by regular way but with the
condition:
"Please do not create sandmin*.in nmode*.in files but use that which are
already in actual directory"
If I am not wrong something like this is possible in mmpbsa.py just by
setting some parameter but
I am not aware of the same possibility in case of mm_pbsa.pl.
Thanks again !
Best wishes,
Marek
Dne Wed, 21 Sep 2011 20:58:53 +0200 Jason Swails <jason.swails.gmail.com>
napsal/-a:
> On Wed, Sep 21, 2011 at 1:56 PM, Marek Maly <marek.maly.ujep.cz> wrote:
>
>> Dear all,
>>
>> I have question about SCEE parameter.
>>
>>
>> I recently did MM/PBSA analyses of my system using mm_pbsa.pl script .
>> I set variable VERBOSE to 1 to have possibilities to check all
>> parameters
>> in intermediate files.
>>
>> For calculation of entropy I used nmode program. What surprised me here
>> was that in output files
>> for sander minimization (sandmin*.out) generated during the calculation
>> I
>> found different value for
>> scee parameter than in case of output files for normal mode calculation
>> (nmode*.out).
>>
>> Below are sandmin*.in and nmode*.in files and relevant parts of both
>> output files mentioned above.
>>
>> As you can see in sandmin*.out is scee=1.2 while in case of nmode*.out
>> there is scee=2.0.
>>
>
> Sure enough... Line 51 of rdinp.f:
>
> rdinp.f:51: scee = 2.0
>
> For some reason the default value for scee is set to 2.0, yet the amber
> force field was parametrized with scee=1.2. However, nmode is not an
> actively maintained program, and there are alternatives to using it for
> normal mode calculations (nab programs, for instance).
>
> However, the issue of the scaling factors is complicated in amber. In
> sander and pmemd, you're allowed a mixed-scaling option in which
> different
> dihedrals can be treated with different scaling constants, primarily to
> enhance the cooperativity of GLYCAM and Amber force fields. However, no
> other programs can handle that currently (including nmode, nab, and I
> believe mdgx as it's released with AmberTools 1.5). Therefore, if you
> get
> the "correct" scaling treatment for your system in sander/pmemd, then you
> will get the wrong (and different) scaling in nmode, since nmode doesn't
> support mixed scaling (so everything will be set to 2.0 and 1.2, or 2.0
> depending on what you set). Therefore, without jumping into the code a
> little bit on your own, there's no way to get entropy contributions using
> mixed-scaling.
>
> I would, however, suggest against using nmode for entropy calculations.
> MMPBSA.py can most likely do what you're trying to do, and it also uses
> the
> more supported and more advanced nab NMODE routines for entropy
> calculations.
>
>
>> To be frank I would assume the same value of scee parameter during all
>> stages of the normal mode calculation,
>> more likely value 1.2 as in my system GAFF (scee=1.2), ff99bsc0
>> (scee=1.2), Glycam_06 (scee=1) forcefields are used.
>>
>> So if nmode scee default value scee=2.0 ? should be changed in my case,
>> how to do it ? I did not find any information
>> about setting this parameter using standard mm_pbsa.pl input file. I
>> guess
>> it could be done by writing this parameter
>> directly in nmode*.in file which is by default created by mm_pbsa.pl
>> script. If I am right, how is then possible to correctly run
>> mm_pbsa.pl with "by hand" created sandmin*.in and nmode*.in files
>> instead
>> of standard mm_pbsa input file ?
>>
>
>
> You could do this, or change the nmode source code above to default to
> 1.2
> by adjusting the line I pointed out above and recompiling.
>
>
>>
>> I would like also to know why sander printed "Note: 1-4 EEL scale
>> factors
>> were NOT found in the topology file.".
>>
>
>> Is it because I am using several ffs which differ in scee (scnb)
>> parameters and for my input files using tleap ( AmberTools 1.4 )
>> instead of sleap ?
>
>
> This was answered in my previous email.
>
> HTH,
> Jason
>
--
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Received on Wed Sep 21 2011 - 16:30:03 PDT
