Hello,
This is threonine.pdb;
ATOM 1 N THR 1 0.080 -0.083 0.000 1.00 0.00
ATOM 2 CA THR 1 1.539 -0.033 0.000 1.00 0.00
ATOM 3 C THR 1 2.032 1.394 0.000 1.00 0.00
ATOM 4 O THR 1 1.268 2.339 0.000 1.00 0.00
ATOM 5 CB THR 1 2.116 -0.818 -1.226 1.00 0.00
ATOM 6 OG1 THR 1 1.743 -2.188 -1.162 1.00 0.00
ATOM 7 CG2 THR 1 3.654 -0.842 -1.361 1.00 0.00
ATOM 8 1H THR 1 -0.523 0.813 0.000 1.00 0.00
ATOM 9 2H THR 1 -0.461 -1.018 0.000 1.00 0.00
ATOM 10 HA THR 1 1.904 -0.508 0.929 1.00 0.00
ATOM 11 HB THR 1 1.691 -0.378 -2.154 1.00 0.00
ATOM 12 HG1 THR 1 2.066 -2.592 -1.973 1.00 0.00
ATOM 13 1HG2 THR 1 3.986 -1.433 -2.235 1.00 0.00
ATOM 14 2HG2 THR 1 4.083 0.168 -1.502 1.00 0.00
ATOM 15 3HG2 THR 1 4.138 -1.279 -0.467 1.00 0.00
ATOM 16 OC THR 1 3.452 1.567 0.000 1.00 0.00
ATOM 17 HC THR 1 3.911 0.645 0.000 1.00 0.00
TER
~
I usedthis command;
antechamber -i threonine.pdb -fi pdb -o threonine.mol2 -fo mol2 -c bcc -s 2
Welcome to antechamber 17.3: molecular input file processor.
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
Status: pass
-- Check Unusual Elements --
Status: pass
-- Check Open Valences --
Status: pass
-- Check Geometry --
for those bonded
for those not bonded
Status: pass
-- Check Weird Bonds --
Status: pass
-- Check Number of Units --
Status: pass
acdoctor mode has completed checking the input file.
Running: /home/roja/amber17_FIRST/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /home/roja/amber17_FIRST/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 64; net charge: 0
Running: /home/roja/amber17_FIRST/bin/sqm -O -i sqm.in -o sqm.out
Running: /home/roja/amber17_FIRST/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC
-o ANTECHAMBER_AM1BCC.AC -f ac -p
/home/roja/amber17_FIRST/dat/antechamber/BCCPARM.DAT -s 2 -j 1
Running: /home/roja/amber17_FIRST/bin/atomtype -f ac -p bcc -o
ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
these are my files;
ANTECHAMBER_AC.AC ANTECHAMBER_AM1BCC_PRE.AC ATOMTYPE.INF sqm.out
threonine.mol2
ANTECHAMBER_AC.AC0 ANTECHAMBER_BOND_TYPE.AC sqm.pdb threonine.pdb
ANTECHAMBER_AM1BCC.AC ANTECHAMBER_BOND_TYPE.AC sqm.in
then i use this command;
parmchk -i threonine.mol2 -f mol2 -o threonine.frcmod
but the threonine.frcmod file is empty;
remark goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
NONBON
~
~
Could you please help me how can i fix it?
With regards
Nick
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Received on Tue Jan 30 2018 - 06:00:02 PST
