Yes, please send the files. Off-list is fine. We think we know what
it is, but want to make sure.
Thanks.
On Thu, Dec 8, 2011 at 7:46 PM, Sai Kumar Ramadugu <sramadugu.gmail.com> wrote:
> 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
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
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>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
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>>
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Dec 08 2011 - 17:30:02 PST
