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
>>
>>
>>
>> Quoting Francesco Pietra <chiendarret.gmail.com>:
>>
>>> Dear Francois:
>>> Attached the two full directories for PHA numbered 1 or 4. I did not
>>> attache the case of PHA #1 ending NH2 instead of NXT because the
>>> result was the same.
>>>
>>> Thanks a lot for your care. What I fear is some silly overlooking
>>> from my side.
>>>
>>> regards
>>> francesco
>>>
>>> On Wed, Oct 6, 2010 at 5:16 PM, FyD <fyd.q4md-forcefieldtools.org>
>>> wrote:
>>>> Francesco,
>>>>
>>>> Could you send to my personal email address a tar.gz file
>>>> - with PHA numbered 4 with your LEaP script, frcmod, PDB file
>>>> etc...
>>>> in one directory (your whole LEaP run 1)
>>>> - with PHA numbered 1 with your LEaP script, frcmod, PDB file
>>>> etc...
>>>> in another directory (your whole LEaP run 2)
>>>>
>>>> I can try to have a look...
>>>>
>>>> regards, Francois
>>>>
>>>>
>>>> Quoting Francesco Pietra <chiendarret.gmail.com>:
>>>>
>>>>> It was a long story and surely tedious to follow by people
>>>>> uninvolved
>>>>> in attempts to generate this new residue in the Amber world. I
>>>>> repeat
>>>>> what I wrote. Leap crashed or, sometimes, hang up (on attempts
>>>>> to load
>>>>> the mol2 file) if PHA residue was numbered 4. If numbered 1, as
>>>>> in the
>>>>> files that I sent, leap produces prmtop/inpcrd. However, these
>>>>> files
>>>>> are not accepted by Chimera ("index out of range"), while VMD
>>>>> shows an
>>>>> extremely distorted molecule, especially as to the NH2 (of
>>>>> CONH2) and
>>>>> phenyl moieties.
>>>>>
>>>>> Susequently I also sent the frcmod file because, of course, it was
>>>>> loaded after the mol2 file in generating prmtop/frcmod.
>>>>>
>>>>> I also saved the *.lib file, if you want to see it.
>>>>>
>>>>> Leap comes from the same compilation, as antechamber, or
>>>>> ambertools
>>>>> 1.2, i.e., fully patched.
>>>>>
>>>>> I also wrote that it is the first time (out of very many) that I
>>>>> encounter such problems (distorted molecule on loading prmtop/
>>>>> inpcrd
>>>>> from antechamber-leap), from Amber 8 to my present version 10. I
>>>>> assumed that VMD is telling the truth.
>>>>>
>>>>> To chck if VMD is posing a false problem, I run antechamber-leap
>>>>> with
>>>>> sustiva.pdb (tutorial b4), encountering no problem. From prmto/
>>>>> inpcrd
>>>>> Chimera showed the arene bonds as pseudobonds, which must be a
>>>>> bug in
>>>>> Chimera as it occurs with all other my mol2 files for aromatic
>>>>> molecules, while VMD showed the molecule correctly. I checked
>>>>> the mol2
>>>>> format against its standard description without detecting
>>>>> anomalies
>>>>> but something wrong must have escaped my attention.
>>>>>
>>>>> thanks for your kind attention
>>>>> francesco
>>>>>
>>>>> On Wed, Oct 6, 2010 at 1:51 PM, FyD <fyd.q4md-
>>>>> forcefieldtools.org> wrote:
>>>>>> Quoting Francesco Pietra <chiendarret.gmail.com>:
>>>>>>
>>>>>>> Sorry, forgot the addendum. Here attached. fc
>>>>>>
>>>>>> oh oh I forgot... When does LEaP crash ?
>>>>>>
>>>>>> I only tested loading only the mol2 file & it works.
>>>>>> I did not load any other file (before or after)...
>>>>>>
>>>>>> PHA = loadmol2 pha.NXT.mol2
>>>>>> => it works for me.
>>>>>>
>>>>>> regards, Francois
>>
>>
>>
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Received on Thu Oct 07 2010 - 09:30:03 PDT
