Hi Lachele,
I have downloaded the bugfix.all with bugfixes upto 22 and the latest
parameter files from glycam.org. I patched the bugfixes and compiled
ambertools 1.5.
I still find the differences that I mentioned in my previous email i.e.,
the angle force constant, equilibrium angle value, NPTRA (number of
dihedral types), additional periodicity and phase values.
Do you want me to send the input and output files off the list?
Let me know.
Regards
Sai
On Thu, Dec 8, 2011 at 2:29 PM, Aron Broom <broomsday.gmail.com> wrote:
> Sai,
>
> Although I have no suggestions for you (and what you are proposing sounds
> totally logical anyway), I'm quite interested in the results as I've also
> been recently using GLYCAM06 with Ambertools 1.5 and all the bug-fixes. I
> didn't think to test the order of force-field importing, but it would be
> quite worthwhile to know if there is a bug.
>
> ~Aron
>
> On Thu, Dec 8, 2011 at 2:59 PM, Sai Kumar Ramadugu <sramadugu.gmail.com
> >wrote:
>
> > Hi Lachele,
> > I have downloaded the latest glycam parameter files. We have AmberTools
> > 1.5 installed with bugfixes upto 7. I used the latest glycam parameters
> to
> > generate the topology and coordinates files with loading glycam first and
> > ff99SB second and vice versa.
> >
> > If I look at the differences in two topology files, the following are
> > different.
> > 1. One of the angle force constant is different ( 50 kcal/mol*rad^2 vs
> 30
> > kcal/mol*rad^2) along with equilibrium angle value (2.094396 rad
> > vs 2.129302 rad)
> > 2. Number of dihedral types (NPTRA) are different 60 vs 61. Since the
> > number of dihedral types are one more than other, there are additional
> > periodicity and phase values added.
> >
> > Now I have downloaded the latest bugfixes that have upto 22 on
> > ambermd.orgwebsite. I'll patch the latest bugfixes and will update you
> > on the list if
> > there are any differences. If I find the differences after the latest
> > bugfixes, then I'll send you the pdb, parm7 and rst7 files for my system.
> >
> >
> > Thank you for your time.
> >
> >
> > Regards
> > Sai
> >
> >
> >
> >
> >
> > On Thu, Dec 8, 2011 at 11:22 AM, Lachele Foley (Lists) <
> lf.list.gmail.com
> > >wrote:
> >
> > > First off, make sure you're using a recent, fully patched version of
> > > AmberTools 1.5. Use tleap or xleap to generate the files (not sleap).
> > > There have been similar issues in the past that were fixed.
> > >
> > > We also recommend using the most up-to-date version of GLYCAM (see
> > > glycam.org/params).
> > >
> > > Ideally, the order doesn't matter, and we try to fix conflicts as soon
> > > as we know about them, but occasionally they happen. In that case, it
> > > is generally better to load ff99SB first and then Glycam. If you are
> > > using the most recent tools and parameters, please give us more
> > > details about the system you are building as well as the versions of
> > > AT and glycam.
> > >
> > >
> > >
> > > On Thu, Dec 8, 2011 at 12:07 PM, Sai Kumar Ramadugu <
> sramadugu.gmail.com
> > >
> > > wrote:
> > > > Dear Amber Users,
> > > > I have a complex of protein with a disaccharide. When I load the
> ff99Sb
> > > > first and GLYCAM second versus GLYCAM first and ff99SB second, the
> > energy
> > > > terms for a zero step minimization in gas phase are different for
> > angle,
> > > > dihedral, 1-4LJ, 1-4Coulomb, and the total potential energy.
> > > > Below are the output values from the respective minimizations:
> > > > 1. ff99SB first, GLYCAM second
> > > >
> > > > NSTEP ENERGY RMS GMAX NAME
> > > > NUMBER
> > > > 1 -1.3061E+03 1.3969E+02 3.4776E+03 SG
> 1025
> > > >
> > > > BOND = 85.4389 ANGLE = 175.7590 DIHED =
> > > > 231.3310
> > > > VDWAALS = 855.0251 EEL = -7406.8357 HBOND =
> > > > 0.0000
> > > > 1-4 VDW = 428.9510 1-4 EEL = 4324.2069 RESTRAINT =
> > > > 0.0000
> > > >
> > > > 2. GLYCAM first and ff99SB second
> > > >
> > > > NSTEP ENERGY RMS GMAX NAME
> > > > NUMBER
> > > > 1 -2.3382E+02 1.3969E+02 3.4776E+03 SG
> 1025
> > > >
> > > > BOND = 85.4389 ANGLE = 170.9682 DIHED =
> > > > 881.3310
> > > > VDWAALS = 855.0251 EEL = -7406.8357 HBOND =
> > > > 0.0000
> > > > 1-4 VDW = 430.1394 1-4 EEL = 4750.1157 RESTRAINT =
> > > > 0.0000
> > > >
> > > >
> > > > The differences appear due to the different values of equilibrium
> angle
> > > > value and force constant value for one atom,
> > > > the dihedral angle force constants and phase are different, the scee
> > and
> > > > scnb values are different after the mixed scaling is included.
> > Therefore
> > > > the respective energy terms are different in the output files.
> > > >
> > > > Is it due to the fact that some of the atomtypes are same in both
> > ff99SB
> > > > and GLYCAM and the parameters get overwritten based on the order of
> > > > inclusion of leaprc files in xleap?
> > > > When I was going through the manual (AmberTools) for carbohydrates,
> the
> > > > order in the manual is load GLYCAM first and ff99SB second.
> > > > Does this mean that whenever you have a protein and sugar complexed,
> > the
> > > > order of leaprc files is always 1st GLYCAM and 2nd ff99SB?
> > > >
> > > > Any suggestions will be helpful.
> > > >
> > > >
> > > > Regards
> > > > Sai
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > >
> > > --
> > > :-) Lachele
> > > Lachele Foley
> > > CCRC/UGA
> > > Athens, GA USA
> > >
> > > _______________________________________________
> > > AMBER mailing list
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> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> >
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Received on Thu Dec 08 2011 - 17:00:02 PST
