Dear All.
I want to simulate a system with its ligands. Ligands are glycerol and
desoxycorticosterone. To prepare the inputs, I followed the instructions at
http://ambermd.org/tutorials/basic/tutorial4/create_prmtop.htm . I splitted
pdb file into three parts where two of them contain only ligands
seperately.
ATOM 2068 C1 1CA A 247 -9.669 -30.195 -21.851 1.00 26.17
C
ATOM 2069 C2 1CA A 247 -10.143 -29.383 -23.056 1.00 26.85
C
ATOM 2070 C3 1CA A 247 -11.556 -28.862 -22.800 1.00 29.65
C
ATOM 2071 C4 1CA A 247 -11.956 -28.557 -21.504 1.00 27.46
C
ATOM 2072 C5 1CA A 247 -11.112 -28.734 -20.413 1.00 25.76
C
ATOM 2073 C6 1CA A 247 -11.623 -28.332 -19.028 1.00 24.16
C
ATOM 2074 C7 1CA A 247 -11.259 -29.375 -17.972 1.00 22.80
C
ATOM 2075 C8 1CA A 247 -9.773 -29.730 -18.038 1.00 23.73
C
ATOM 2076 C9 1CA A 247 -9.464 -30.354 -19.402 1.00 24.99
C
ATOM 2077 C10 1CA A 247 -9.733 -29.384 -20.556 1.00 24.39
C
ATOM 2078 C11 1CA A 247 -8.037 -30.910 -19.462 1.00 24.90
C
ATOM 2079 C12 1CA A 247 -7.778 -31.925 -18.345 1.00 23.64
C
ATOM 2080 C13 1CA A 247 -8.036 -31.258 -16.993 1.00 25.19
C
ATOM 2081 C14 1CA A 247 -9.482 -30.769 -16.954 1.00 24.25
C
ATOM 2082 C15 1CA A 247 -9.581 -30.263 -15.515 1.00 25.28
C
ATOM 2083 C16 1CA A 247 -8.860 -31.367 -14.735 1.00 28.25
C
ATOM 2084 C17 1CA A 247 -8.148 -32.209 -15.799 1.00 26.28
C
ATOM 2085 C18 1CA A 247 -7.052 -30.116 -16.731 1.00 19.48
C
ATOM 2086 C19 1CA A 247 -8.681 -28.273 -20.568 1.00 22.66
C
ATOM 2087 C20 1CA A 247 -6.788 -32.689 -15.290 1.00 26.82
C
ATOM 2088 C21 1CA A 247 -6.080 -33.822 -16.038 1.00 25.81
C
ATOM 2089 O3 1CA A 247 -12.349 -28.746 -23.733 1.00 32.88
O
ATOM 2090 O20 1CA A 247 -6.289 -32.178 -14.289 1.00 28.16
O
ATOM 2091 O21 1CA A 247 -4.729 -33.980 -15.601 1.00 26.05
O
is the pdb file for desoxycorticosterone. When I run
antechamber -i 2Q3Y-ligand-ica.pdb -fi pdb -o 2Q3Y-ligand-ica.mol2 -fo mol2
-c bcc -s 2
and receive
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Unrecognized atomic name , exit
Running: /home/batu/Desktop/master/software/amber14/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Unrecognized atomic name , exitTotal number of electrons: 0; net
charge: 0
Running: /home/batu/Desktop/master/software/amber14/bin/sqm -O -i sqm.in -o
sqm.out
At line 580 of file sqm.F90
Fortran runtime error: End of file
Error: cannot run "/home/batu/Desktop/master/software/amber14/bin/sqm -O -i
sqm.in -o sqm.out" of bcc() in charge.c properly, exit
If I change ATOM type to HETATM I end up with
Running: /home/batu/Desktop/master/software/amber14/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
Be cautious, use a large value of PSCUTOFF (>100) will significantly
increase the computation time
Running: /home/batu/Desktop/master/software/amber14/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 150; net charge: 0
Running: /home/batu/Desktop/master/software/amber14/bin/sqm -O -i sqm.in -o
sqm.out
Error: cannot run "/home/batu/Desktop/master/software/amber14/bin/sqm -O -i
sqm.in -o sqm.out" of bcc() in charge.c properly, exit
I am totally new to AMBER and simulated structures without ligand so far,
so I couldn't deal with this problem. What might be wrong with my
submission?
Thank you,
Batuhan
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Received on Wed Aug 20 2014 - 11:00:06 PDT
