[gmx-users] Re: amb2gmx.pl to convert GLYCAM topology

[Alan]

Thanks Yun,

Have a look at http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx so
you may have tips of how to improve you check. One thing I recorded that
makes diff is that amber input files have 6 decimals of precision and
PDB/GRO only 3.

Not knowing exactly what you did, but it sounds that 0.05% (for total pot
energy?) is OK.

Alan



On 15 September 2011 06:18, Yun Shi <yunshi09 at gmail.com> wrote:

> Hi Alan,
>
> For example, in the Glycam_06g.dat file, you can find:
> ........
> OH-CG-CG-OS   1   -1.10          0.0            -1
> ........
>
> So this dihedral parameter has a force constant of -1.10, and this is what
> I mean by "GLYCAM force field assigns negative force constants to some
> dihedrals".
>
> I did try the GMX45 approach, and using the conversion factor 4.184, I got
> a difference of about 0.05%.  I am not sure if this is caused not setting
> step size in the sander minimization.
>
> Regards,
> Yun
>
>
>
>
>
>
>
> Date: Tue, 13 Sep 2011 12:03:10 +0100
> From: Alan <alanwilter at gmail.com>
> Subject: Re: [gmx-users] Re: amb2gmx.pl to convert GLYCAM topology
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <CAEznbznq98PbHjdR1SMPOgdTz_pGFqsk40iZLfPQ7-NiZywJ4A at mail.gmail.com
> >
> Content-Type: text/plain; charset="utf-8"
>
>
> Hi Yun,
>
> Have you read http://ambermd.org/formats.html?
>
> In particular, this note:
>
> """
> NOTE: *the atom numbers in the following arrays that describe bonds,
> angles,
> and dihedrals are coordinate array indexes for runtime speed. The true atom
> number equals the absolute value of the number divided by three, plus one.
> In the case of the dihedrals, if the fourth atom is negative, this implies
> that the dihedral is an improper. If the third atom is negative, this
> implies that the end group interations are to be ignored. End group
> interactions are ignored, for example, in dihedrals of various ring systems
> (to prevent double counting of 1-4 interactions) and in multiterm
> dihedrals.
> *
> """
>
> I may be failing to understand what you mean by "GLYCAM force field assigns
> negative force constants to some dihedrals".
>
> Anyway, since GMX 4.5 can go without RB convertions, you can do this:
>
> acpype -x disac.inpcrd -p disac.prmtop --gmx45
>
> If you have sander, you can do just one step of EM and compare against one
> step EM with GMX. Do the proper conversions and Energies diff should be <
> 0.001%.
>
> Cheers,
>
> Alan
>
> On 12 September 2011 21:21, Yun Shi <yunshi09 at gmail.com> wrote:
>
> > Hi all,
> >
> > I am not a CS person, but I did find something in acpype.py as
> >
> > .............
> >                 if phase in [0, 180]:
> >                     properDihedralsGmx45.append([
>
>> item[0].atoms, phaseRaw,
>> > kPhi, period])
>> >                     if not self.gmx45:
>> >                         if kPhi > 0: V[period] = 2 * kPhi * cal
>> >                         if period == 1:
>> >                             C[0] += 0.5 * V[period]
>> >                             if phase == 0:
>> >                                 C[1] -= 0.5 * V[period]
>> >                             else:
>> >                                 C[1] += 0.5 * V[period]
>> >                         elif period == 2:
>> > ......................
>> >
>> > kPhi here seems to be the dihedral force constant, and it seems if kPhi
>> <
>> > 0, no value will be assigned to C[0], C[1], C[2] ...
>> >
>> > I wonder if the negative dihedral force constants problem could be
>> solved
>> > by changing 'kPhi > 0' to 'kPhi != 0' for acpype?
>> >
>> > Thanks,
>> >
>> > Yun
>> >
>> > --
>> > gmx-users mailing list    gmx-users at 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-request at gromacs.org.
>> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >
>>
>>
>>
>> --
>> Alan Wilter SOUSA da SILVA, DSc
>> Bioinformatician, UniProt - PANDA, EMBL-EBI
>> CB10 1SD, Hinxton, Cambridge, UK
>> +44 1223 49 4588
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110913/f9bc31d1/attachment-0001.html
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Tue, 13 Sep 2011 16:46:44 +0530
>> From: om prakash <ombioinfo at gmail.com>
>> Subject: [gmx-users] Unsubscribe me Please
>>
>> To: gmx-users at gromacs.org
>> Message-ID:
>>        <CAM5rxXNDPYi_aEEd+7efAmZoPex8B4Um5FwgJKg6hfm=
>> t9YUOg at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Unsubscribe me Please
>> --
>> Om Prakash Sharma
>> Ph.D Scholar & DIT JRF
>> Centre for Bioinformatics
>> Pondicherry University
>> Pondicherry-605014
>> -------------- next part --------------
>
>
> --
> gmx-users mailing list    gmx-users at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110915/697d5019/attachment.html>