Re: [AMBER] Cpptraj failure

From: Lin Song <linsong234.gmail.com>
Date: Mon, 13 Jul 2015 12:14:42 -0400

Thanks, Dan. I did some modification and regenerated the prmtop and pdb file, and it works.

Regards,

Lin
On Jul 2, 2015, at 12:45, Daniel Roe <daniel.r.roe.gmail.com> wrote:

> 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,
>>
>> 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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>
>
> --
> -------------------------
> 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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> http://lists.ambermd.org/mailman/listinfo/amber


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Received on Mon Jul 13 2015 - 09:30:05 PDT
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