[gmx-users] Conversion of the GLYCAM dihedral parameters

sa sagmx.mail at gmail.com
Mon Aug 8 17:07:43 CEST 2011 

>
> Thank you Olivier for your response.
>

SA



> ------------------------------
>
> Message: 2
> Date: Thu, 28 Jul 2011 11:20:44 +0100
> From: Oliver Grant <olivercgrant at gmail.com>
> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <CAFd05fG5yAzPHr=sSfiCaA0FF0Q7UEt3ib_YJrs70qME3N3afg at mail.gmail.com
> >
> Content-Type: text/plain; charset="windows-1252"
>
> Hi SA,
>
> I think this is due to the original amb2gmx.pl coder only considering
> AMBER
> type dihedrals. He/She didn't expect any negative values. You'll notice
> certain groups like NAc and COO- on sugars are affected when you run your
> simulation. Below is a similar post with a fix to the amb2gmx.pl code.
> It's
> short so I pasted it rather than linking.
>
> You may already know this but note also the default is to correctly fudge
> AMBERS 1-4 interactions. So if you run a sugar using the GLYCAM forcefield
> they will be incorrectly scaled/fudged. An easy fix is to copy the
> ffamber99sb.itp (may be called something else now) to your local directory
> where you are running the md and change to:
>
> [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> 1               2                         yes                     1.0
> 1.0
>
> If you have a sugar and a protein you cannot mix the scaling. Mixed scaling
> is possible in amber11 if you really need it. I did all this when 4.0.7 was
> the latest release so things may have changed and it may now be possible to
> mix scaling or it may be that something else has changed :)
>
> If you find anything when testing the parameters please do post back.
> All the best,
> Oliver
>
>
>
> *Hi all,
>
> There is a problem that I encountered when I was trying to manually
> verify the proper dihedral conversion from AMBER topology to GROMACS
> topology using amb2gmx perl script.
> Some of the dihedrals were set to zero by amb2gmx even if in the
> prmtop file they were not zero. This was happening for all the lines
> that had PK with negative values!. Reading the script I came up with
> the following lines for V[i] calculation (lines 749  to 755 in the
> script file):
>
> ...........................
>
>  # get all force constants for each line of a dihedral #
>  my $lines = $i -1 +$numijkl;
>  for(my $j=$i;$j<=$lines;$j++){
>   my $period = abs($pn{$j});
>   if($pk{$j}>0) {
>     $V[$period] = 2*$pk{$j}*$cal/$idivf{$j};
>   }
>
> ...........................
>
> It seems from here that only PK values > 0 are considered when
> computing the RB constants.
> After I change the ">" sign to "!=" (i.e. not equal to) everything
> goes fine and ALL the dihedral are transformed correctly.
>
> While this is OK with different  AMBER sets and GAFF if one wish to
> convert a GLYCAM (which comes also with Amber package) generated
> topology, in the gromacs resultant file there will be missing
> parameters for dihedrals. That's because GLYCAM does not use phase
> shift and have also negative values for several PK
>
> Is this a bug or there is a reason for considering only the positive
> values of PK or I am missing something (as I am a begginer with
> AMBER)?
> (or maybe amb2gmx was designed only to work an AMBER ff conversion and
> not for example GLYCAM)
>
> Thanks for any comment,
> Andrei*
>
>
> On 21 July 2011 10:48, sa <sagmx.mail at gmail.com> wrote:
>
> > Yeah I have also found this page. Finally I did the conversion. I am
> >> currently testing the parameters.
> >>
> >
> > Thank you  Austin and Mark for your help
> >
> > SA-
> >
> >>
> >> ------------------------------
> >>
> >> Message: 4
> >> Date: Wed, 20 Jul 2011 07:17:18 -0700 (PDT)
> >> From: "Austin B. Yongye" <ybausty at yahoo.com>
> >> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
> >>        in the  GROMACS format.
> >> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >> Message-ID:
> >>        <1311171438.14853.YahooMailClassic at web161422.mail.bf1.yahoo.com>
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >> > So my questions are: how to convert it in the gromacs format ?
> >> I haven't done AMBER to GROMACS conversions. But a google search led me
> to
> >> this page. It's just a matter of knowing the different formats.
> >>
> >> http://ffamber.cnsm.csulb.edu
> >>
> >> > Is it correct to use the absolute value of the multiplicity in my
> >> parameters and use the negative values of barrier heights when they are
> >> exist in the AMBER parameters? Since, I have noticed that in the AMBER
> >> ff port in GROMACS, the multiplicity values are always set to > 0
> >> and   the barrier heights have sometime a negative value.
> >>
> >>
> >>
> >> So my questions are: how to convert it in the gromacs format ?  Is it
> >> correct to use the absolute value of the multiplicity in my parameters
> and
> >> use the negative values of barrier heights when they are exist in the
> AMBER
> >> parameters? Since, I have noticed that in the AMBER ff port in GROMACS,
> the
> >> multiplicity values are always set to > 0 and   the barrier heights have
> >> sometime a negative value.
> >>
> >>
> >> Thank you again for your advice.
> >>
> >> SA-
> >>
> >>
> >>
> >>
> >> Message: 1
> >>
> >> Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT)
> >>
> >> From: "Austin B. Yongye" <ybausty at yahoo.com>
> >>
> >> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
> >>
> >>         in the  GROMACS format.
> >>
> >> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >>
> >> Message-ID:
> >>
> >>         <1311098935.93905.YahooMailClassic at web161426.mail.bf1.yahoo.com
> >
> >>
> >> Content-Type: text/plain; charset="utf-8"
> >>
> >>
> >>
> >> It is normal to have combinations of negative and positive values for
> the
> >> barrier heights. Those are just the best coefficients to reproduce some
> QM
> >> rotational energy curve during the parameterization.  The negative
> >> periodicities are a convention from AMBER. They simply indicate that the
> >> dihedral angle potential has more than one term. For your example below:
> >>
> >>
> >>
> >>
> >> O2-P
> >>
> >>           -OS-CP   1    0.10          0.0            -3.
> Dimethyl
> >> phosphate
> >>
> >>                              1   -0.50          0.0            -2.
> >>
> >>
> >>
> >>           1    0.10
> >>
> >>           0.0             1
> >>
> >> -3, -2 and 1 signify V3, V2 and V1 terms, respectively. Once a positive
> >> value is reached, terms for the O2-P-OS-CP potential have been
> completely
> >> accounted for.
> >>
> >>
> >>
> >> Hope that helps.
> >>
> >> Austin-
> >>
> >>
> >>
> >>
> >>
> >> --- On Tue, 7/19/11, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> >>
> >>
> >>
> >> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> >>
> >> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in
> >> the GROMACS format.
> >>
> >> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> >>
> >> Date: Tuesday, July 19, 2011, 7:08 AM
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>     On 19/07/2011 11:56 PM, sa wrote:
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>       Dear
> >>
> >>           GROMCS users,
> >>
> >>
> >>
> >>       I
> >>
> >>           am trying to convert some GLYCAM parameters in GROMACS format.
> >>
> >>           For this
> >>
> >>           purpose, I am using the latest GLYCAM parameters downloaded
> >>
> >>           from the RJ. Woods’
> >>
> >>           website and the examples given in the acpype code (here for
> >>
> >>           the dihedral angles) :
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9&r=9&redir=1
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>       -------------------
> >>
> >> # dihedral    idivf        barrier hight/2 kcal/mol  phase degrees
> >> periodicity     comments
> >>
> >>        X -ca-ca-X    4           14.500*                     180.000
> >>          2.000             intrpol.bsd.on C6H6
> >>
> >>
> >>
> >> * to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in
> >> topolbuild, why?) = 30.334 or 15.167 kJ/mol
> >>
> >> # X -CA-CA-X    4   14.50        180.0             2.
> >> intrpol.bsd.on C6H6 (from parm99.dat)
> >>
> >>
> >>
> >> # X-CA-CA-X     3    30.33400     0.00000   -30.33400     0.00000
> >> 0.00000     0.00000   ; intrpol.bsd.on C6H6
> >>
> >>
> >>
> >> -----------
> >>
> >>
> >>
> >>       I have no problems with the parameters for proteins. But, in case
> of
> >> the GLYCAM parameters, I am a little confused
> >>
> >>
> >>
> >> about the conversion of dihedral force constants (DFC), especially when
> >> the DFC and the periodicity values are < 0 for example
> >>
> >> for this torsion:
> >>
> >>
> >>
> >>
> >>
> >>       O2-P
> >>
> >>           -OS-CP   1    0.10          0.0            -3.
> Dimethyl
> >> phosphate
> >>
> >>                     1   -0.50          0.0            -2.
> >>
> >>
> >>
> >>           1    0.10
> >>
> >>           0.0             1
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>     Where only a positive value makes sense, sometimes people use
> >>
> >>     negative values to indicate some special functional form. This can
> >>
> >>     be easier to code. Regardless, you'll have to check out the GLYCAM
> >>
> >>     documentation and see what is meant, before you can address how to
> >>
> >>     convert it into a GROMACS format. Obviously the contents of parts of
> >>
> >>     chapter 4 and 5 of the manual will be important.
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>     Mark
> >>
> >>
> >>
> >>
> >>
> >> -----Inline Attachment Follows-----
> >>
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