> > Thank you Olivier for your response. > SA
> ------------------------------ > > Message: 2 > Date: Thu, 28 Jul 2011 11:20:44 +0100 > From: Oliver Grant <[email protected]> > Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <CAFd05fG5yAzPHr=ssficaa0ff0q7uet3ib_yjrs70qme3n3...@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 <[email protected]> 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" <[email protected]> > >> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters > >> in the GROMACS format. > >> To: Discussion list for GROMACS users <[email protected]> > >> Message-ID: > >> <[email protected]> > >> 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" <[email protected]> > >> > >> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters > >> > >> in the GROMACS format. > >> > >> To: Discussion list for GROMACS users <[email protected]> > >> > >> Message-ID: > >> > >> <[email protected] > > > >> > >> 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 <[email protected]> wrote: > >> > >> > >> > >> From: Mark Abraham <[email protected]> > >> > >> Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in > >> the GROMACS format. > >> > >> To: "Discussion list for GROMACS users" <[email protected]> > >> > >> 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 [email protected] > >> 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 [email protected]. > >> Can't post? 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