On Wed, Aug 3, 2011 at 6:08 AM, Massimiliano Porrini <mozz76.gmail.com>wrote:
> Dear Jason,
>
> Many thanks for spending time to check my files.
> The seh.lib was created by me with tleap (for several reason I couldn't use
> xleap).
>
tleap and xleap are the same core source code. xleap just has a couple
extra calls to graphical libraries, but any file created by the 2 should be
identical as long as you do the same thing in each session.
>
> And from your comments I understood the mistakes I did in creating the
> library.
>
> A)
>
> The fragment peptide had number 12 in its pdb (because I extracted it
> from the original whole pdb) and, instead of using this
> command:
>
It's far more typical to create a fragment library from a mol2 file or some
other file with atomic charges. How did you set atomic charges in your
molecule? In any case, if you have antechamber create a mol2 file, then
this indexing issue will disappear.
>
> bond name.SEH.anum1 name.SEH.anum2 ,
>
> I used the following:
>
> bond name.12.anum1 name.12.anum2
>
> thinking that it would not eventually matter for the lib file.
>
>
> B)
>
> While I was creating the bond between atoms number 3 and 4 a doubt
> crossed my mind: I thought to re-create the bond but double, as they are
> C and O (respectively) atoms of the carbonyl group and I assumed that
> the last action with tleap would have overwritten the previous one, so that
> to have
> a double bond between C and O (but instead the result was 1+2=3).
>
It appeared as though the bond was already there. When you issued the
command twice, it added 2 more bonds. Keep in mind that the Amber force
field has no knowledge/concept of "bond order". A bond either exists or it
doesn't -- there's no distinction between a "single" and "double" (or
aromatic 1.5 bond order) in the code itself. The only difference this will
cause is reflected in a shorter/longer and weaker/stronger bond.
>
>
> I am going to regenerate from scratch the seh.lib with AT 1.5 just
> installed in my machine though.
>
> To this point I have three more questions:
>
> 1) Do I have to define the carbonyl bond as double or single?
>
If the bond doesn't exist already, then create it *once*. It appears as
though tleap chokes on this (although sleap handles it correctly it would
appear). Every bond loaded as a force field library should have each and
every existing bond defined *once*.
>
> 2) Since my modified residue is a serine at the neutral C-terminus (i.e.
> with such an end -COOH),
> do I have to define the "tail" anyway? And if yes, is this tail still the
> carbonyl C?
>
No. If it shouldn't have a tail, don't give it a tail.
>
> 3) Why do you think I need a frcmod file? Probably I am missing something
> here, but once I
> define the atom types of my modified residue as those included in
> ff99SBildn (and I believe I can
> do that because I have only one more proton at the end that I can define as
> the 'HO' atom type,
> like in the case of GLH or ASH), don't they already exist in the related
> parameters file?
> As a matter of fact I had created also the coordinate and topology files of
> my peptide without
> using the seh.lib, but just executing one by one all the needed commands in
> tleap and at the end
> I ran "check" and all the FF parameters resulted defined.
>
Here is the error I got via tleap after I fixed your seh.library file (to
the one I attached to my last email):
> saveamberparm pep prmtop inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: 1.000000 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: OH - CT - HC
Could not find angle parameter: OH - CT - HC
Building proper torsion parameters.
Building improper torsion parameters.
total 33 improper torsions applied
Building H-Bond parameters.
Parameter file was not saved.
> quit
Quit
As you can see, it could not find the OH-CT-HC angle parameter, so you have
to provide this via an frcmod file.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Aug 03 2011 - 07:00:04 PDT
