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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Received on Wed Oct 06 2010 - 01:30:03 PDT
