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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>>
>
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>
F.-Y. Dupradeau
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Received on Wed Oct 06 2010 - 02:30:04 PDT
