[gmx-users] Conversion of the GLYCAM dihedral parameters
Oliver Grant
olivercgrant at gmail.com
Thu Jul 28 12:20:44 CEST 2011
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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