[AMBER] Cpptraj failure

From: Lin Song <linsong234.gmail.com>
Date: Tue, 30 Jun 2015 22:47:37 -0400

Hi all,

Iím trying to use AmberTools15 Cpptraj (version 15) to translate molecule back to the primary box. But when I load my prmtop file, it shows the following error:

Error: Atom 5620 was assigned a lower molecule # than previous atom. This can
Error: happen if 1) bond information is incorrect or missing, or 2) if the
Error: atom numbering in molecules is not sequential. If topology did not
Error: originally contain bond info, 1) can potentially be fixed by
Error: increasing the bondsearch cutoff offset (currently 0.200). 2) can be
Error: fixed by either using the 'fixatomorder' command, or using
Error: the 'setMolecules' command in parmed.py.
Error: Could not determine molecule information for 2v5w_solv.prmtop.
Error: SetSolventInfo: No molecule information.
Error: Could not determine solvent information for 2v5w_solv.prmtop.

The system is a protein-ligand complex. Atom 5620 is the first atom of my ligand. Following is part of the pdb:

ATOM 5610 CG2 VAL 363 -22.703 12.060 -15.908 1.00 0.00
ATOM 5611 HG21 VAL 363 -23.719 11.983 -16.297 1.00 0.00
ATOM 5612 HG22 VAL 363 -22.654 12.896 -15.208 1.00 0.00
ATOM 5613 HG23 VAL 363 -22.021 12.249 -16.738 1.00 0.00
ATOM 5614 C VAL 363 -20.885 11.780 -13.432 1.00 0.00
ATOM 5615 O VAL 363 -21.484 11.417 -12.422 1.00 0.00
ATOM 5616 OXT VAL 363 -20.265 12.841 -13.437 1.00 0.00
TER
ATOM 5617 ZN ZN1 364 1.737 -5.728 -0.585 1.00 0.00
TER
ATOM 5618 K K 365 -2.061 -2.044 -5.375 1.00 0.00
TER
ATOM 5619 K K 366 -16.372 2.374 -5.270 1.00 0.00
TER
ATOM 5620 HH31 ACE 367 -11.422 -18.799 -2.103 1.00 0.00
ATOM 5621 CH3 ACE 367 -10.801 -18.127 -2.658 1.00 0.00
ATOM 5622 HH32 ACE 367 -11.410 -17.383 -3.128 1.00 0.00
ATOM 5623 HH33 ACE 367 -10.264 -18.673 -3.406 1.00 0.00
ATOM 5624 C ACE 367 -9.827 -17.462 -1.728 1.00 0.00
ATOM 5625 O ACE 367 -9.006 -16.644 -2.137 1.00 0.00
ATOM 5626 N ARG 368 -9.623 -18.112 -0.583 1.00 0.00
ATOM 5627 H ARG 368 -10.419 -17.873 -0.027 1.00 0.00

And if I use Amber12 Cpptraj (Version 12.4), it completes normally. My input file is as follows:

trajin prod.rst restart
center :1-372 mass
image center familiar
trajout prod_center.rst restart

Can I trust Amber12 Cpptraj result? And why does AmberTools15 give that error?
Any help would be appreciated.

Thanks,
Lin
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Received on Tue Jun 30 2015 - 20:00:03 PDT
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