AMBER Archive (2006)

Subject: AMBER: a ligand file

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Tue Sep 05 2006 - 15:18:51 CDT

Dear All,

I have the cAMP ligand pdb file:

HETATM 2187 P CMP 450 110.710 60.550 12.724
 1.00 27.15 P

HETATM 2188 O1P CMP 450 109.482 60.586 11.899
 1.00 28.83 O

HETATM 2189 O2P CMP 450 111.217 59.250 13.220
 1.00 29.28 O

HETATM 2190 O5* CMP 450 110.514 61.516 13.987
 1.00 31.82 O

HETATM 2191 C5* CMP 450 111.645 62.155 14.614
 1.00 29.57 C

HETATM 2192 C4* CMP 450 112.486 62.788 13.543
 1.00 28.12 C

HETATM 2193 O4* CMP 450 113.703 63.417 14.020
 1.00 26.33 O

HETATM 2194 C3* CMP 450 113.023 61.750 12.591
 1.00 29.42 C

HETATM 2195 O3* CMP 450 111.896 61.256 11.885
 1.00 32.45 O

HETATM 2196 C2* CMP 450 114.053 62.566 11.817
 1.00 29.36 C

HETATM 2197 O2* CMP 450 113.461 63.405 10.840
 1.00 30.00 O

HETATM 2198 C1* CMP 450 114.632 63.437 12.943
 1.00 27.81 C

HETATM 2199 N9 CMP 450 115.952 63.013 13.416
 1.00 28.21 N

HETATM 2200 C8 CMP 450 117.069 63.805 13.482
 1.00 27.03 C

HETATM 2201 N7 CMP 450 118.143 63.174 13.883
 1.00 28.87 N

HETATM 2202 C5 CMP 450 117.703 61.883 14.117
 1.00 28.77 C

HETATM 2203 C6 CMP 450 118.369 60.731 14.569
 1.00 32.68 C

HETATM 2204 N6 CMP 450 119.661 60.709 14.899
 1.00 28.97 N

HETATM 2205 N1 CMP 450 117.647 59.589 14.680
 1.00 32.51 N

HETATM 2206 C2 CMP 450 116.347 59.627 14.375
 1.00 28.97 C

HETATM 2207 N3 CMP 450 115.607 60.655 13.953
 1.00 32.26 N

HETATM 2208 C4 CMP 450 116.354 61.766 13.839
 1.00 28.26 C

CONECT 2187 2188 2189 2190 2195
                         

CONECT 2188 2187
                         

CONECT 2189 2187
                         

CONECT 2190 2187 2191
                         

CONECT 2191 2190 2192
                         

CONECT 2192 2191 2193 2194
                         

CONECT 2193 2192 2198
                         

CONECT 2194 2192 2195 2196
                         

CONECT 2195 2187 2194
                         

CONECT 2196 2194 2197 2198
                         

CONECT 2197 2196
                         

CONECT 2198 2193 2196 2199
                         

CONECT 2199 2198 2200 2208
                         

CONECT 2200 2199 2201
                         

CONECT 2201 2200 2202
                         

CONECT 2202 2201 2203 2208
                         

CONECT 2203 2202 2204 2205
                         

CONECT 2204 2203
                         

CONECT 2205 2203 2206
                         

CONECT 2206 2205 2207
                         

CONECT 2207 2206 2208
                         

CONECT 2208 2199 2202 2207

TER

END

I want to run a MD on protein cAMP ligand interaction.

When I use ANTECHAMBER to get the prepin file,
ANTECHAMBER says the bondtype cannot be run. Will you
tell me what should I do in oreder to get the cAMP
prepin file.

The command is:

$AMBERHOME/exe/antechamber -i cAMP.pdb -fi pdb -o
cAMP.prepin -fo prepi -c bcc -s 2

Running: /home/local/amber9/exebondtype -i
ANTECHAMBER_BOND_TYPE.ACO -o ANTECHAMBER_BOND_TYPE.AC
-f ac -j full

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 MAXUTOFF in define.h and recompile
bondtype.C
(4) increase PSCUTOFF in define.h and recompile
bondtype.C

Be cautious, use a large value of PSCUTOFF (>10) will
significantly increase the computer time

Error: cannot run "/home/localamber9/exebondtype -i
ANTECHAMBER_BOND_TYPE.ACO -o ANTECHAMBER_BOND_TYPE.AC
-f ac -j full: in judgebondtype () of antechamber.c
properly, exit

I also try to use xleap to add the H to the cAMP,
however xleap cannot do that because there is no cAMP
residue.

In addition, if you can tell me something on how to
combine
the original protein-cAMP complex PDB file and the
newly produced ligand prepin file in the xleap, it
will be much better.

I am looking forward to getting your message.

Best regards.

Sincerely yours,

Fenghui Fan

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