Amin,
I forward the q4mdfft email to the Amber mailing list to answer to
your queries...
regards, Francois
----- Forwarded message from fyd.q4md-forcefieldtools.org -----
Date: Sun, 04 May 2014 14:00:08 +0200
From: FyD <fyd.q4md-forcefieldtools.org>
Reply-To: q4md-fft.q4md-forcefieldtools.org, FyD
<fyd.q4md-forcefieldtools.org>
Subject: Re: [q4md-fft] FAD parameters from F-90
To: q4md-fft.q4md-forcefieldtools.org, amin.imtech.res.in
Dear Amin,
> I think you would have to write a REDDB for Dummies for me.
I know ;-) We plan to update this F-90 project...
We are going to release a new version of RED Server Dev/PyRED
> Here is what I did
>
> grep -v "to be replaced by the correct tripos" script1.ff >
> script1-new.ff
> perl -p -i.old -e 's/##!# //g' script1-new.ff
> tleap -f script1-new.ff
> #started tleap
> tleap -f leaprc.ff99SB
> frcmod = loadamberparams script3.ff
-> see in script1.ff: script3.ff is already loaded...
> loadoff = q4md-forcefieldtools-cofactors.off
> fad = loadmol2 FAD.mol2 (This FAD.mol2 is the one generated on running
> tleap -f script1-new.ff)
the ff lib is loaded twice: (i) q4md-forcefieldtools-cofactors.off and
(ii) FAD.mol2
an off file and mol2 file have the same role: a FF library
I would do:
grep -v "to be replaced by the correct tripos" script1.ff > script1-new.ff
perl -p -i.old -e 's/##!# //g' script1-new.ff
perl -p -i.old -e 's/\#\#\#\#\#\# //g' script1-new.ff
tleap -f script1-new.ff
all should be ok...
q4md-forcefieldtools-cofactors.off is generated and can be used in
another tleap run...
> check fad
>
> Doing this I get lots and lots of missing angles. Can you please tell me
> my mistake here.
see above
> Finally I have a problem where I would simulate FAD bound to a protein
> like the problem mentioned at
> http://archive.ambermd.org/201303/0118.html. So i will later try to have
> FAD as a single residue.
yes! but RED Server Dev/PyRED does all this problem by now...
regards, Francois
> On 2014-05-04 11:29, FyD wrote:
>
>> Dear Amin,
>>
>> Please have a look at the script1.ff LEaP script in F-90:
>> have a look at the script1.ff LEaP script in F-90:
>> http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff [1]
>>
>> a frcmod file is automatically loaded:
>> http://q4md-forcefieldtools.org/REDDB/projects/F-90/script3.ff [2]apply:
>> grep -v "to be replaced by the correct tripos" script1.ff > script1-new.ff
>> perl -p -i.old -e 's/##!# //g' script1-new.ff
>>
>> see once again: script1.ff all is explained in this file...
>>
>> I hope this helps...
>>
>> regards, Francois
>>
>>> I am trying to use FAD parameters from the project F-90. I was
>>> having problems with my pdb of FAD most likely because of wrong
>>> atom names. Just to check, I saved the mol2 file of FAD from the
>>> project as pdb and loaded it in leap along with the .off file
>>> generated after running script1. However, on checking this file I
>>> get some missing angles Checking for angle parameters. Could not
>>> find angle parameter: NC - CB - CA Could not find angle
>>> parameter: CB - NC - CB Could not find angle parameter: CB - N*
>>> - CB Could not find angle parameter: N* - CB - CA Could not find
>>> angle parameter: C - CB - NC Could not find angle parameter: C -
>>> NC - CB Could not find angle parameter: NC - C - NA I am using
>>> the parameters from an REDDB project for the first time so I may
>>> be doing something really silly. Any help would be highly
>>> appreciated.
>
> Links:
> ------
> [1] http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff
> [2] http://q4md-forcefieldtools.org/REDDB/projects/F-90/script3.ff
----- End forwarded message -----
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Received on Sun May 04 2014 - 22:30:02 PDT
