<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;">Yeah I have also found this page. Finally I did the conversion. I am currently testing the parameters. <br>
</blockquote><div><br>Thank you Austin and Mark for your help<br><br>SA-<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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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 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 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.<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 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:<br>
<br>
<br>
<br>
<br>
O2-P<br>
<br>
-OS-CP 1 0.10 0.0 -3. Dimethyl 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 value is reached, terms for the O2-P-OS-CP potential have been completely 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 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>
<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 periodicity comments<br>
<br>
X -ca-ca-X 4 14.500* 180.000 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 topolbuild, why?) = 30.334 or 15.167 kJ/mol<br>
<br>
# X -CA-CA-X 4 14.50 180.0 2. intrpol.bsd.on C6H6 (from parm99.dat)<br>
<br>
<br>
<br>
# X-CA-CA-X 3 30.33400 0.00000 -30.33400 0.00000 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 the GLYCAM parameters, I am a little confused<br>
<br>
<br>
<br>
about the conversion of dihedral force constants (DFC), especially when 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 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>
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