I think the problems were unrelated; the fixatomorder command adjusted
the .prmtop file appropriately, and adding the title line to the .mdcrd
file started the trajin read at the beginning of the molecule. I'll go
back and look at my input files, I don't remember a -A flag, but.....
Thanks, Tom P.
On 8/16/16 10:56 AM, Daniel Roe wrote:
> On Tue, Aug 16, 2016 at 8:20 AM, Thomas Pochapsky <pochapsk.brandeis.edu> wrote:
>> I think I answered my own question, but for the record, the .mdcrd files
>> generated by sander (AMBER14) need a blank line at the top of the file
>> to be read correctly using trajin, at least with a .prmtop of older
>> vintage. We found this to be true if you want to import .mdcrd files as
>> .trj files into PyMOL as well.
> This is because the Amber ASCII trajectory format requires a title
> line (see http://ambermd.org/formats.html#trajectory).
>
> I'm not clear on how you got a trajectory file with no title (perhaps
> you used the '-A' command line flag with a non-existent trajectory
> file?) or how adding a title to your trajectory file would fix a
> topology with molecules having non-contiguous atoms.
>
> -Dan
>
>>
>>
>> -------- Forwarded Message --------
>> Subject: cpptraj issues
>> Date: Fri, 12 Aug 2016 12:52:19 -0400
>> From: Thomas Pochapsky <pochapsk.brandeis.edu>
>> To: AMBER Mailing List <amber.ambermd.org>
>>
>>
>>
>> When attempting to load a .prmtop file into cpptraj, I get the following
>> error message:
>>
>> Error: Atom 6415 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 MycGMIV.prmtop.
>> Error: SetSolventInfo: No molecule information.
>> Error: Could not determine solvent information for MycGMIV.prmtop.
>>
>> I tried 'fixatomorder", no difference.
>>
>> If it helps, atom 6415 is the first K+ ion used to solvate and balance
>> charge.
>>
>> Any suggestions?
>>
>> Thanks,
>> Tom Pochapsky
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Tue Aug 16 2016 - 08:30:02 PDT
