On Thu, Oct 7, 2010 at 7:17 PM, Paul S. Nerenberg <psn.berkeley.edu> wrote:
> Hi Francesco,
>
> I have read back through all of your entries regarding this issue,
> Hopefully this is what you're after, but if not, apologies for the
> diversion...
>
> Best,
>
> Paul
Hello Paul:
I had badly searched for the phenylalanine amide residue through
Amber. Thanks a lot for showing so clearly how to do.
Learning from scratch how to build a new residue was no lost time,
however, as I have also other unusually modified residues, including
chirality inversion at CA. First I'll try your leap scripts against
the latter problem.
all the best
francesco
>
>
>
>
> On Oct 7, 2010, at 9:14 AM, Paul S. Nerenberg wrote:
>
>> Francesco,
>>
>> Actually, I'm still a bit confused about what you want to do here. Is
>> this the same C-terminal phenylalanine amide residue that you were
>> looking at with another program several weeks ago? If so, then there
>> is no reason to be jumping through any of these (increasingly
>> elaborate) hoops. The AMBER ff99SB force field already includes a
>> definition for the amidated C-terminus (NHE). You just need your
>> sequence (either in a PDB file or manually in leap) to end with PHE
>> NHE -- this will build phenylalanine as the last residue with an NH2
>> "residue" attached to its C-terminus.
>>
>> Best,
>>
>> Paul
>>
>>
>> On Oct 7, 2010, at 8:08 AM, Francesco Pietra wrote:
>>
>>> Dear Francois:
>>> I forgot the main question following your discovery that ff99SB should
>>> not be loaded to leap in my case. That is, do you believe that the
>>> gaff-only route is a viable route to prepare the new residue
>>> phenylalanine amide? I plan to add the new residue to the standard
>>> residues in an Amber ff (ideally ff99SB) so that my peptide containing
>>> the new residue is recognized by leap.
>>>
>>> thanks
>>> francesco
>>>
>>>
>>> ---------- Forwarded message ----------
>>> From: Francesco Pietra <chiendarret.gmail.com>
>>> Date: Thu, Oct 7, 2010 at 4:57 PM
>>> Subject: Re: [AMBER] Incorrect handling of phenylalanine amide by
>>> antechamber
>>> To: AMBER Mailing List <amber.ambermd.org>
>>>
>>>
>>> Dear Francois:
>>> Thanks a lot. Plase see below.
>>>
>>> On Thu, Oct 7, 2010 at 11:56 AM, FyD <fyd.q4md-forcefieldtools.org>
>>> wrote:
>>>>
>>>> Dear Francesco,
>>>>
>>>> I tested your two sets of data & this is exactly what I told you in
>>>> my
>>>> first email: Antechamber authorizes non-strict mol2 file format. I
>>>> think this is potentially buggy if one wants to use the outputs of
>>>> Antechamber in other programs.
>>>
>>> Perhaps worth knowing that when I said that this is the first time
>>> (out of very many) that antechamber outputs are not perfect for leap,
>>> the "very many" were always for organic natural products, or their
>>> modification. This is the first time I used Antechamber for a modified
>>> amino acids. See below comments about not loading ff99SB.
>>>>
>>>> When your mol2 file format has a residue number = 4, LEaP crashes
>>>> (because a patch was not applied; I think you did not applied the
>>>> patch suggested by Dr Case).
>>>
>>> As I wrote, I applied all current bugfixes (1-35) and recompiled
>>> ambertools/gcc and amber/gfortran (previously I had only applied
>>> bugfixes 1-5 and compiled all intel/mkl. Still. leap crashed when
>>> PHA#4.
>>>>
>>>> When your mol2 file has a residue number = 1, LEaP does not crash. I
>>>> only loaded gaff and the geometry of PHA is correct (correct in LEaP,
>>>> in VMD using the prmtop/inpcrd generated, correct when using ambpdb &
>>>> the prmtop/inpcrd generated).
>>>>
>>>> I did not load amber99SB & then gaff - if you do so and if the
>>>> geometry looks broken this is just another bug or an incompatibility
>>>> between the leaprc of amber99SB and gaff.
>>>
>>> I had suggested in one in my mails if it is worth trying to load gaff
>>> alone. As I had no reply, I thought it was a bad idea (it is common
>>> knowledge that gaff was made to be compatible with amber ffs) and did
>>> not try.
>>>>
>>>> regards, Francois
>
>
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Received on Thu Oct 07 2010 - 13:30:03 PDT
