Sorry, forgot the addendum. Here attached. fc
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret.gmail.com>
Date: Wed, Oct 6, 2010 at 12:07 PM
Subject: Re: [AMBER] Fwd: Incorrect handling of phenylalanine amide by
antechamber
To: AMBER Mailing List <amber.ambermd.org>
hello:
Thanks for your kind offer. Attached please find the pdbs (ending NXT
or not) and the mol2 from the NXT. I used antechamber 1.2 fully
patched and gcc compiled on amd64.
francesco
On Wed, Oct 6, 2010 at 11:29 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Francesco,
>
>> I forgot: also, even the mol2 file generated by antechamber is
>> accepted by Chimera, extrapolating what I said below.
>
> So ?
>
> This is not because Antechamber generates a mol2 file that is
> recognized by Chimera, (VMD, insightII... whatever) that this mol2
> file will indeed be recognized by LEaP... There are bugs everywhere
> here - in all the programs (for instance VMD (64 bits) used to not
> handle mol2 files composed by a single atom).
>
> Can you post your mol2 file so that we can try to "finish" this problem ?
>
> regards, Francois
>
>> ---------- Forwarded message ----------
>> From: Francesco Pietra <chiendarret.gmail.com>
>> Date: Wed, Oct 6, 2010 at 10:21 AM
>> Subject: Re: [AMBER] Incorrect handling of phenylalanine amide by antechamber
>> To: AMBER Mailing List <amber.ambermd.org>
>>
>>
>> I agree, however the starting pdb has no problems with even Chimera.
>> In my experience, any but slight deviation from standard will not be
>> accepted by Chimera, which follows a cliche of standard for amino
>> acids, peptides and proteins (while VMD accepts nearly every deviation
>> from standard). Also, I have taken the information for the CONH2 from
>> amino acids that have such functionality in the side chain. What
>> remains, is the standard for phenylalanine. That to explain why at the
>> moment I have no better ideas.
>>
>> My further attempts to generate prmtop/inpcrd file is that I have my
>> proven program for simulated annealing (i.e., conformational search)
>> which only accepts such an input. Otherwise I had already turned to
>> other approaches to the conformational problem of the peptide that
>> contains Fa.
>>
>> thanks
>> francesco
>>
>> On Wed, Oct 6, 2010 at 8:19 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>>> Dear Francesco,
>>>
>>>> By using exactly the same procedure below, I started by renaming atoms
>>>> of NH2 (of CONH2) NXT HXT1 HXT2. Same error in prmtop/inpcrd: ring and
>>>> NH2 of CONH2 highly deformed. Notice that, again, residue PHA in the
>>>> pdb file had to be renumbered from 4 to 1, otherwise xleap crashes
>>>> when attempting to load the mol2 file obtained with antechamber.
>>>
>>> When Antechamber and the R.E.D. Tools have to build a FF library a
>>> common problem is ... the input file, itself, provided by the user -
>>> and even by a novice user. In a FF lib, the topology (usually defined
>>> from a correct input geometry), atom & residue names (two atom names
>>> in a residue cannot share the same name) and atom equivalencing (used
>>> in charge equivalencing) have to be correctly defined. As a new user
>>> does not have any idea about these rules, the PDB file she/he provides
>>> as input is often "broken" or does not follow a standard format. Thus,
>>> Antechamber and the R.E.D. Tools have to deals with these problems and
>>> the number of problems to handle is quite a challenge.
>>>
>>> To solve these numerous problems one has two options:
>>> (1) One tries to make the program compatible with the numerous inputs
>>> provided and one generates the FF library following the information
>>> available in the input. I think this is the approach followed by
>>> Antechamber. A problem here is that a FF library does not always have
>>> a strict format. Consequently, the file might be recognized by a
>>> program such as VMD and not by another one such as LEaP...
>>> (2) One corrects the input provided so that one generates a FF library
>>> in a strict format which in principle is compatible with all programs.
>>> This is the approach followed in Ante_R.E.D. 2.0/R.E.D. IV. This will
>>> be available in R.E.D. Server 2.0. We are late and it will be released
>>> soon.
>>>
>>> regards, Francois
>>>
>>>
>>>
>>> _______________________________________________
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>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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>
>
>
> F.-Y. Dupradeau
> ---
> http://q4md-forcefieldtools.org/FyD/
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Received on Wed Oct 06 2010 - 04:30:03 PDT
