Hi Ben,
>> Error here: a CT1 atom name should not be present in the unique column
>> of atom name of the PDB file format...
>
> Why is this? I realise this is a stupid question, so apologies, but
> I'm not entirely sure I understand.
The strategy is:
Ante_R.E.D. R.E.D. LEaP
PDB input file(s) ----> P2N file(s) ----> mol2 file(s) ----> prmtop
(mol3 files(s)) prmcrd
NEVER LOADING A P2N FILE IN LEAP !!!
-1- in a PDB file, LEaP does not handle/not understand the atoms that
share the same name in a given residue.
-2- Ante_R.E.D. takes the unique atom name column of the PDB input
file and move it in the red column (column on the righ; see
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#EXAMPLE-P2N-FILE;
besides Ante_R.E.D. 2.0 checks/corrects duplicated atom names in the
red column) and creates a new column of atom names (yellow column)
reflecting chemical equivalencing.
In the P2N file, in the yellow column atom names which are
chemically equivalent (to be used by R.E.D. for RESP input generation)
should bear the same name! A "T" is also added to CH2 and CH3 carbons.
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#ATOM-NAME
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#RULES
In your former email, you reported that Leap displayed a warning about
a "CT1 atom name": this likely means that you loaded a P2N file as PDB
file in LEaP; LEaP do not know about the red column in a P2N file, and
read only the yellow one. If this is indeed a P2N file, this likely
means that you have in the yellow column atom names which have
identical atom names (reflecting chemical equivalencing) and LEaP will
modify them. I think this is your problem...
I hope it is clear; not that easy to explain ;-)
regards, Francois
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Received on Sat Jan 07 2012 - 01:00:03 PST
