Dear Jason,
I'm very thankful for the answers to my questions.
Eventually I recreated my seh.lib file from scratch, applying the correct
directives and it works perfectly now.
As far as the frcmod file is concerned you were right. The thing is
that I had erroneously defined
the -CH_2 hydrogens as HC, while they are H1 type.
So the OH - CT - H1 angles parameters are now included in 99SBildn force field.
Just for curiosity and to totally clarify the issue I have one more question:
In AmberTools Users' Manual, pag. 54, the LEaP command "bond" allows one to
define also the bond order (single, double, triple and aromatic).
I am wondering why, when (as you wrote previously) amber FF just needs to know
what is bonded to what and the bond order will be considered via force
constants and
equilibrium distances.
Thank you so much again for your help.
Regards,
M
2011/8/3 Jason Swails <jason.swails.gmail.com>:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr Massimiliano Porrini
Institute for Condensed Matter and Complex Systems
School of Physics & Astronomy
The University of Edinburgh
James Clerk Maxwell Building
The King's Buildings
Mayfield Road
Edinburgh EH9 3JZ
Tel +44-(0)131-650-5229
E-mails : M.Porrini.ed.ac.uk
mozz76.gmail.com
maxp.iesl.forth.gr
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Received on Wed Aug 03 2011 - 08:30:02 PDT
