On Wed, 2014-08-20 at 20:59 +0300, BATUHAN KAV wrote:
> 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
>
The problem with pasting a PDB file to an email like this is that we can
never be sure what the original format was, since email clients often do
us the favor of reformatting and automatic line breaking. However, it
looks like there is only one space between ATOM and 2091 in that last
line. If that's the case, your PDB file is broken. The PDB file is
quite strict with respect to what it expects to find in certain columns.
What this means is that either:
1. The program that generated this PDB file for you is broken.
2. When you edited the PDB file, you did it wrong. An example is
replacing "HETATM" with "ATOM" instead of "ATOM " (notice the two extra
spaces in "ATOM " so that both strings are 6 characters wide).
In any case, you will need to fix this before proceeding.
> 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
And this error message seems to confirm that the PDB file is broken.
> If I change ATOM type to HETATM I end up with
Perhaps this is simply reversing a change you had already made before?
>
> 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
The actual error will be in sqm.out. Look for an error message toward
the bottom of that file, and see if any relevant information comes up if
you try to google that error message.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 20 2014 - 11:30:03 PDT
