Cpptraj from AT 12 (several years old at this point) simply did not look
for this error. This kind of issue can happen sometimes with tleap when
residues are bonded outside the normal head/tail (e.g. disulfide bonds).
You can use the parmed command checkvalidity (I think) for independent
confirmation. As the error message indicates, the fixatomorder command can
be used to correctly reorder the topology and coordinates.
-Dan
On Tuesday, June 30, 2015, Lin Song <linsong234.gmail.com> wrote:
> Hi all,
>
> I’m 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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> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jul 02 2015 - 10:00:03 PDT
