<div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Thank you Olivier for your response. <br></blockquote><div><br>SA <br>
</div><div><br> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
------------------------------<br>
<br>
Message: 2<br>
Date: Thu, 28 Jul 2011 11:20:44 +0100<br>
From: Oliver Grant <<a href="mailto:olivercgrant@gmail.com">olivercgrant@gmail.com</a>><br>
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<CAFd05fG5yAzPHr=<a href="mailto:sSfiCaA0FF0Q7UEt3ib_YJrs70qME3N3afg@mail.gmail.com">sSfiCaA0FF0Q7UEt3ib_YJrs70qME3N3afg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
Hi SA,<br>
<br>
I think this is due to the original <a href="http://amb2gmx.pl" target="_blank">amb2gmx.pl</a> coder only considering AMBER<br>
type dihedrals. He/She didn't expect any negative values. You'll notice<br>
certain groups like NAc and COO- on sugars are affected when you run your<br>
simulation. Below is a similar post with a fix to the <a href="http://amb2gmx.pl" target="_blank">amb2gmx.pl</a> code. It's<br>
short so I pasted it rather than linking.<br>
<br>
You may already know this but note also the default is to correctly fudge<br>
AMBERS 1-4 interactions. So if you run a sugar using the GLYCAM forcefield<br>
they will be incorrectly scaled/fudged. An easy fix is to copy the<br>
ffamber99sb.itp (may be called something else now) to your local directory<br>
where you are running the md and change to:<br>
<br>
[ defaults ]<br>
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>
1 2 yes 1.0<br>
1.0<br>
<br>
If you have a sugar and a protein you cannot mix the scaling. Mixed scaling<br>
is possible in amber11 if you really need it. I did all this when 4.0.7 was<br>
the latest release so things may have changed and it may now be possible to<br>
mix scaling or it may be that something else has changed :)<br>
<br>
If you find anything when testing the parameters please do post back.<br>
All the best,<br>
Oliver<br>
<br>
<br>
<br>
*Hi all,<br>
<br>
There is a problem that I encountered when I was trying to manually<br>
verify the proper dihedral conversion from AMBER topology to GROMACS<br>
topology using amb2gmx perl script.<br>
Some of the dihedrals were set to zero by amb2gmx even if in the<br>
prmtop file they were not zero. This was happening for all the lines<br>
that had PK with negative values!. Reading the script I came up with<br>
the following lines for V[i] calculation (lines 749 to 755 in the<br>
script file):<br>
<br>
...........................<br>
<br>
# get all force constants for each line of a dihedral #<br>
my $lines = $i -1 +$numijkl;<br>
for(my $j=$i;$j<=$lines;$j++){<br>
my $period = abs($pn{$j});<br>
if($pk{$j}>0) {<br>
$V[$period] = 2*$pk{$j}*$cal/$idivf{$j};<br>
}<br>
<br>
...........................<br>
<br>
It seems from here that only PK values > 0 are considered when<br>
computing the RB constants.<br>
After I change the ">" sign to "!=" (i.e. not equal to) everything<br>
goes fine and ALL the dihedral are transformed correctly.<br>
<br>
While this is OK with different AMBER sets and GAFF if one wish to<br>
convert a GLYCAM (which comes also with Amber package) generated<br>
topology, in the gromacs resultant file there will be missing<br>
parameters for dihedrals. That's because GLYCAM does not use phase<br>
shift and have also negative values for several PK<br>
<br>
Is this a bug or there is a reason for considering only the positive<br>
values of PK or I am missing something (as I am a begginer with<br>
AMBER)?<br>
(or maybe amb2gmx was designed only to work an AMBER ff conversion and<br>
not for example GLYCAM)<br>
<br>
Thanks for any comment,<br>
Andrei*<br>
<br>
<br>
On 21 July 2011 10:48, sa <<a href="mailto:sagmx.mail@gmail.com">sagmx.mail@gmail.com</a>> wrote:<br>
<br>
> Yeah I have also found this page. Finally I did the conversion. I am<br>
>> currently testing the parameters.<br>
>><br>
><br>
> Thank you Austin and Mark for your help<br>
><br>
> SA-<br>
><br>
>><br>
>> ------------------------------<br>
>><br>
>> Message: 4<br>
>> Date: Wed, 20 Jul 2011 07:17:18 -0700 (PDT)<br>
>> From: "Austin B. Yongye" <<a href="mailto:ybausty@yahoo.com">ybausty@yahoo.com</a>><br>
>> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters<br>
>> in the GROMACS format.<br>
>> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
>> Message-ID:<br>
>> <<a href="mailto:1311171438.14853.YahooMailClassic@web161422.mail.bf1.yahoo.com">1311171438.14853.YahooMailClassic@web161422.mail.bf1.yahoo.com</a>><br>
>> Content-Type: text/plain; charset="utf-8"<br>
>><br>
>> > So my questions are: how to convert it in the gromacs format ?<br>
>> I haven't done AMBER to GROMACS conversions. But a google search led me to<br>
>> this page. It's just a matter of knowing the different formats.<br>
>><br>
>> <a href="http://ffamber.cnsm.csulb.edu" target="_blank">http://ffamber.cnsm.csulb.edu</a><br>
>><br>
>> > Is it correct to use the absolute value of the multiplicity in my<br>
>> parameters and use the negative values of barrier heights when they are<br>
>> exist in the AMBER parameters? Since, I have noticed that in the AMBER<br>
>> ff port in GROMACS, the multiplicity values are always set to > 0<br>
>> and the barrier heights have sometime a negative value.<br>
>><br>
>><br>
>><br>
>> So my questions are: how to convert it in the gromacs format ? Is it<br>
>> correct to use the absolute value of the multiplicity in my parameters and<br>
>> use the negative values of barrier heights when they are exist in the AMBER<br>
>> parameters? Since, I have noticed that in the AMBER ff port in GROMACS, the<br>
>> multiplicity values are always set to > 0 and the barrier heights have<br>
>> sometime a negative value.<br>
>><br>
>><br>
>> Thank you again for your advice.<br>
>><br>
>> SA-<br>
>><br>
>><br>
>><br>
>><br>
>> Message: 1<br>
>><br>
>> Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT)<br>
>><br>
>> From: "Austin B. Yongye" <<a href="mailto:ybausty@yahoo.com">ybausty@yahoo.com</a>><br>
>><br>
>> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters<br>
>><br>
>> in the GROMACS format.<br>
>><br>
>> To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
>><br>
>> Message-ID:<br>
>><br>
>> <<a href="mailto:1311098935.93905.YahooMailClassic@web161426.mail.bf1.yahoo.com">1311098935.93905.YahooMailClassic@web161426.mail.bf1.yahoo.com</a>><br>
>><br>
>> Content-Type: text/plain; charset="utf-8"<br>
>><br>
>><br>
>><br>
>> It is normal to have combinations of negative and positive values for the<br>
>> barrier heights. Those are just the best coefficients to reproduce some QM<br>
>> rotational energy curve during the parameterization. The negative<br>
>> periodicities are a convention from AMBER. They simply indicate that the<br>
>> dihedral angle potential has more than one term. For your example below:<br>
>><br>
>><br>
>><br>
>><br>
>> O2-P<br>
>><br>
>> -OS-CP 1 0.10 0.0 -3. Dimethyl<br>
>> phosphate<br>
>><br>
>> 1 -0.50 0.0 -2.<br>
>><br>
>><br>
>><br>
>> 1 0.10<br>
>><br>
>> 0.0 1<br>
>><br>
>> -3, -2 and 1 signify V3, V2 and V1 terms, respectively. Once a positive<br>
>> value is reached, terms for the O2-P-OS-CP potential have been completely<br>
>> accounted for.<br>
>><br>
>><br>
>><br>
>> Hope that helps.<br>
>><br>
>> Austin-<br>
>><br>
>><br>
>><br>
>><br>
>><br>
>> --- On Tue, 7/19/11, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br>
>><br>
>><br>
>><br>
>> From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
>><br>
>> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in<br>
>> the GROMACS format.<br>
>><br>
>> To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
>><br>
>> Date: Tuesday, July 19, 2011, 7:08 AM<br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>> On 19/07/2011 11:56 PM, sa wrote:<br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>> Dear<br>
>><br>
>> GROMCS users,<br>
>><br>
>><br>
>><br>
>> I<br>
>><br>
>> am trying to convert some GLYCAM parameters in GROMACS format.<br>
>><br>
>> For this<br>
>><br>
>> purpose, I am using the latest GLYCAM parameters downloaded<br>
>><br>
>> from the RJ. Woods’<br>
>><br>
>> website and the examples given in the acpype code (here for<br>
>><br>
>> the dihedral angles) :<br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>> <a href="http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9&r=9&redir=1" target="_blank">http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9&r=9&redir=1</a><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>> -------------------<br>
>><br>
>> # dihedral idivf barrier hight/2 kcal/mol phase degrees<br>
>> periodicity comments<br>
>><br>
>> X -ca-ca-X 4 14.500* 180.000<br>
>> 2.000 intrpol.bsd.on C6H6<br>
>><br>
>><br>
>><br>
>> * to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in<br>
>> topolbuild, why?) = 30.334 or 15.167 kJ/mol<br>
>><br>
>> # X -CA-CA-X 4 14.50 180.0 2.<br>
>> intrpol.bsd.on C6H6 (from parm99.dat)<br>
>><br>
>><br>
>><br>
>> # X-CA-CA-X 3 30.33400 0.00000 -30.33400 0.00000<br>
>> 0.00000 0.00000 ; intrpol.bsd.on C6H6<br>
>><br>
>><br>
>><br>
>> -----------<br>
>><br>
>><br>
>><br>
>> I have no problems with the parameters for proteins. But, in case of<br>
>> the GLYCAM parameters, I am a little confused<br>
>><br>
>><br>
>><br>
>> about the conversion of dihedral force constants (DFC), especially when<br>
>> the DFC and the periodicity values are < 0 for example<br>
>><br>
>> for this torsion:<br>
>><br>
>><br>
>><br>
>><br>
>><br>
>> O2-P<br>
>><br>
>> -OS-CP 1 0.10 0.0 -3. Dimethyl<br>
>> phosphate<br>
>><br>
>> 1 -0.50 0.0 -2.<br>
>><br>
>><br>
>><br>
>> 1 0.10<br>
>><br>
>> 0.0 1<br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>> Where only a positive value makes sense, sometimes people use<br>
>><br>
>> negative values to indicate some special functional form. This can<br>
>><br>
>> be easier to code. Regardless, you'll have to check out the GLYCAM<br>
>><br>
>> documentation and see what is meant, before you can address how to<br>
>><br>
>> convert it into a GROMACS format. Obviously the contents of parts of<br>
>><br>
>> chapter 4 and 5 of the manual will be important.<br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>> Mark<br>
>><br>
>><br>
>><br>
>><br>
>><br>
>> -----Inline Attachment Follows-----<br>
>><br>
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