Dear All,I got following warning while running antechamber for ligand preparation.
saman.mcg18:/data-store/ds_Working_sya/modelling-t.b.ptr1/2X9G/LY1/test> ./antec
hamber
Running: /usr/local/amber14/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o
?ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /usr/local/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC
.AC -p gaff
Total number of electrons: 224; net charge: 0
Running: /usr/local/amber14/bin/sqm -O -i sqm.in -o sqm.out
Running: /usr/local/amber14/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMB
ER_AM1BCC.AC -f ac -p /usr/local/amber14/dat/antechamber/BCCPARM.DAT -s 2 -j 1
Running: /usr/local/amber14/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -
i ANTECHAMBER_AM1BCC_PRE.AC
Running: /usr/local/amber14/bin/prepgen -i ANTECHAMBER_PREP.AC -f car -o LY1.pre
pin -rn "LY1" -rf molecule.res
Warning: ATOM N16 has unfilled valence, assuming the linked atom name (in other
residue) is "M"
???????? change "M" to "-M" if ATOM N16 is linked to the immediate previous resi
due
???????? change "M" to "+M" if ATOM N16 is linked to the immediate after residue.I have added hydrogen in ligand using structure editing command chimera, before adding hydrogen I have modify atom typing of nitrogen atom and oxygen atoms of carbonyl carbon using setattr command of chimera. Then I checked coordinates of atoms and matched with pdb file coordinates of ligand atoms. Prepin and frcmod file are generated perfectly with out any change in coordinates. Should I safely ignore above error or it may cause trouble during md? Please suggests your views.
Thanks
Best Regards,
Saman Yousuf Ali
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Received on Tue Feb 21 2017 - 22:30:03 PST
