> > 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" <ybau...@yahoo.com> > Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters > in the GROMACS format. > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <1311171438.14853.yahoomailclas...@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" <ybau...@yahoo.com> > > Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters > > in the GROMACS format. > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Message-ID: > > <1311098935.93905.yahoomailclas...@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.abra...@anu.edu.au> wrote: > > > > From: Mark Abraham <mark.abra...@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@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----- > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? 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