Dear David,
I am getting similar error/warnings while I was playing with isoG. I did
double check inside mol2 file for any structure problem, even I tried
pdb file format but it doesn't help.
Antachamber is behaving kind of wiered with this molecules.
I tested mol2 file with "acdoctor" it also gave bunch of warnings.
-- Check Open Valences --
Warning: the number of bonded atoms (2) for atom (ID: 3, Name: N1) does not match
the desired connectivity (3) based on the atom type (N) defined in CORR_NAME_TYPE.DAT.
Warning: the number of bonded atoms (2) for atom (ID: 6, Name: N2) does not match
the desired connectivity (3) based on the atom type (N) defined in CORR_NAME_TYPE.DAT.
BUT, You may safely ingnor the warnings if your input molecule uses atom names or element as atom types
-- check weird bonds --
Error: weird atomic valence (5) for atom (ID: 7, Name: C3), please check atomic connectivity
After conversion of mol2 file into ac type error was changed.
Error: weird atomic valence (1) for atom (ID: 1, Name: C),
possible have open valence
But, when I manually defined all bond types, exclusively in single and
double bond terms instead of aromatic bond types error was gone for ac
file using acdoctor.
During prepi file preparation from ac, I got similar warning irrelevant
of bond types defined, as it was mentioned in this post.
Warning: ATOM N2 has unfilled valence, assuming the linked atom name (in other residue) is "M"
change "M" to "-M" if ATOM N2 is linked to the immediate previous residue
change "M" to "+M" if ATOM N2 is linked to the immediate after residue
Now, my main question is can I parametrize this molecule with this error? if yes then will this molecules behave correctly in sander/pmemd? I am sure this molecules doesn't have any open valence and also you can see the attached hydrogens in connectivity section in mol2 and ac file.
Many thanks.
Ashish Radadiya
PDRA, Cardiff University
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Received on Thu Jun 15 2017 - 06:30:03 PDT
