Ok, problem solved. The call to parmchk just needed to be changed as
follows:
parmchk -i <mol2name> -f mol2 -o <frcmodname> -p
$AMBERHOME/dat/leap/parm/parm10.dat
the default is to pass "-p gaff.dat". Maybe this could be bypassed by not
creating an frcmod, but I couldn't get the types loaded from leaprc.ff10 to
match those assigned in tleap.
Regardless, I think my ends have been achieved.
Brian
On Tue, Jul 2, 2013 at 9:34 AM, Brian Radak <radak004.umn.edu> wrote:
> Thanks for the quick replies.
>
> On closer inspection it would appear that all hydrogens are getting typed
> correctly (*i.e.* the specific type is indicative of the connectivity),
> but hydrogens bound to carbon all get the "HC"-type LJ parameters
> (hydrogens bound to nitrogen are just fine). I don't have much interest in
> figuring out what is going on in PARMCHK.DAT in order to fix this (does
> anybody know what the tables in there mean?).
>
> Fortunately parmed should let me just correct the LJ parameters based on a
> type selection. Unfortunately, I'm not sure the ".%" ambmask syntax is
> working properly in the Python implementation at the moment and Jason is
> out of the office for the week.
>
> I guess I can just do this by hand in tleap.
>
> Brian
>
>
> On Tue, Jul 2, 2013 at 3:45 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Brian,
>>
>> There is no difficulty for differentiating the 'HC' atom type vs the
>> 'H1', 'H2' or 'H3' ones; i.e. is a given hydrogen atom, which is
>> connected to a carbon atom connected to one, two or three heteroatoms.
>> The same rule applies for the aromatic hydrogens 'HA', vs 'H4' and
>> 'H5'... These 'HC' vs 'H1'/'H2'/'H3' and 'HA' vs 'H4'/'H5' definitions
>> are at the basis of the Cornell et al. force field; and there is no
>> difficulty for coding that...
>>
>> R.E.D. Python fully handles this quite basic problem (differentiating
>> the different double bonds is far more complex for instance); I invite
>> you to use R.E.D. Python when available i.e. sometimes next
>> September/October 2013.
>> You can also use R.E.D. Server and request a private assistance to
>> post-process your data with R.E.D. Python.
>>
>> regards, Francois
>>
>>
>> > I'm running calculations on a bunch of nucleic acids and analogues.
>> Since
>> > these are non-standard non-nucleobase compounds I used antechamber to
>> > assign atom types. However, it would appear that the hydrogen
>> Lennard-Jones
>> > parameters for atoms of the same type do not match in prmtops generated
>> > from antechamber files and those from leaprc.ff10
>> >
>> > (using parmed.py printDetails)
>> > Rmin/2 epsilon
>> > type AC FF10 AC FF10
>> > H4 1.4870 1.4090 0.0157 0.0150
>> > HA 1.4870 1.4590 0.0157 0.0150
>> >
>> > I'm guessing I messed something up here by reloading parameters. Should
>> I
>> > not be creating a new frcmod? Still, I find it weird that two atoms
>> would
>> > have the same type but different parameters. Where does the flag "-at
>> > amber" get parameters from? I assumed these would be the same LJ types
>> that
>> > have been around since FF94.
>>
>>
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for
> Integrative Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute
> appropriate address.
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Tue Jul 02 2013 - 07:30:02 PDT
