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 Tue Oct 05 2010 - 23:30:02 PDT
