AMBER Archive (2008)

Subject: AMBER: Problems simulating a protein-ligand complex

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Fri Jun 06 2008 - 12:55:05 CDT

Hi all,
I'm trying to run simulation of a protein in complex with GTP, a small
nucleoside triphosphate. One of the tutorials (#5) contains a
description of the procedure for generating prmtop and inpcrd files for
organic molecules (I assume that once that step is completed, the two
prmtop/inpcrd sets from the protein and the ligand can be combined using
xleap, correct?).

I tried this approach, but antechamber fails with the following error
message:

Running: /opt/amber/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -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 MAXVASTATE 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 "/opt/amber/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0
-o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in judgebondtype() of
antechamber.c properly, exit

The structure has correct connectivity and came directly from a PDB
file. Since the ligand PDB file is not that large, I'm pasting it below.
Thank you for any suggestions.

Sasha

HETATM 1343 PB GDP 180 62.667 77.781 47.505 1.00 31.08
P
HETATM 1344 O1B GDP 180 61.587 77.413 46.626 1.00 30.69
O
HETATM 1345 O2B GDP 180 63.294 79.098 47.336 1.00 24.13
O
HETATM 1346 O3B GDP 180 63.804 76.731 47.410 1.00 29.87
O
HETATM 1347 O3A GDP 180 62.281 77.644 49.012 1.00 29.39
O
HETATM 1348 PA GDP 180 62.781 76.563 50.116 1.00 32.94
P
HETATM 1349 O1A GDP 180 64.200 76.858 50.463 1.00 38.15
O
HETATM 1350 O2A GDP 180 62.459 75.187 49.671 1.00 39.73
O
HETATM 1351 O5' GDP 180 61.927 76.929 51.222 1.00 37.11
O
HETATM 1352 C5' GDP 180 61.690 78.290 51.572 1.00 37.93
C
HETATM 1353 C4' GDP 180 61.260 78.393 53.002 1.00 36.58
C
HETATM 1354 O4' GDP 180 59.989 77.748 53.185 1.00 40.35
O
HETATM 1355 C3' GDP 180 62.181 77.747 54.015 1.00 36.25
C
HETATM 1356 O3' GDP 180 62.291 78.499 55.179 1.00 38.09
O
HETATM 1357 C2' GDP 180 61.548 76.420 54.295 1.00 39.40
C
HETATM 1358 O2' GDP 180 61.846 76.085 55.643 1.00 43.75
O
HETATM 1359 C1' GDP 180 60.078 76.792 54.224 1.00 40.06
C
HETATM 1360 N9 GDP 180 59.258 75.630 53.844 1.00 39.43
N
HETATM 1361 C8 GDP 180 59.255 75.041 52.612 1.00 38.59
C
HETATM 1362 N7 GDP 180 58.334 74.158 52.460 1.00 38.35
N
HETATM 1363 C5 GDP 180 57.550 74.278 53.590 1.00 35.85
C
HETATM 1364 C6 GDP 180 56.499 73.638 53.877 1.00 37.59
C
HETATM 1365 O6 GDP 180 56.005 72.734 53.233 1.00 39.03
O
HETATM 1366 N1 GDP 180 55.907 74.049 55.053 1.00 38.56
N
HETATM 1367 C2 GDP 180 56.436 74.939 55.901 1.00 36.65
C
HETATM 1368 N2 GDP 180 55.747 75.129 57.025 1.00 34.76
N
HETATM 1369 N3 GDP 180 57.574 75.569 55.662 1.00 37.24
N
HETATM 1370 C4 GDP 180 58.110 75.138 54.493 1.00 37.60
C
CONECT 1343 1344 1345 1346
1347
CONECT 1344
1343
CONECT 1345
1343
CONECT 1346
1343
CONECT 1347 1343
1348
CONECT 1348 1347 1349 1350
1351
CONECT 1349
1348
CONECT 1350
1348
CONECT 1351 1348
1352
CONECT 1352 1351
1353
CONECT 1353 1352 1354
1355
CONECT 1354 1353
1359
CONECT 1355 1353 1356
1357
CONECT 1356
1355
CONECT 1357 1355 1358
1359
CONECT 1358
1357
CONECT 1359 1354 1357
1360
CONECT 1360 1359 1361
1370
CONECT 1361 1360
1362
CONECT 1362 1361
1363
CONECT 1363 1362 1364
1370
CONECT 1364 1363 1365
1366
CONECT 1365
1364
CONECT 1366 1364
1367
CONECT 1367 1366 1368
1369
CONECT 1368
1367
CONECT 1369 1367
1370
CONECT 1370 1360 1363
1369
MASTER 308 1 2 4 6 2 0 6 1447 1 28
15
END

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