Hi,
The 'keepext' option was introduced in version 16. You could download
the GitHub version and compile it and use that maybe.
-Dan
PS - Thanks for pointing out that cpptraj doesn't complain about
unprocessed args for the trajectory commands, I need to fix that...
On Wed, Nov 15, 2017 at 7:16 AM, Lizelle Lubbe <LBBLIZ002.myuct.ac.za> wrote:
> Hi David,
>
> I am using cpptraj version 15 available at our high performance computing centre
>
> It doesn't mention any arguments not being processed. This is from the cpptraj_output:
>
> OUTPUT TRAJECTORIES:
> 'md2_9_stripped_snapshot.pdb' is a PDB file (1 file per frame), writing charges to occupancy column and vdW radii to B-factor column, using PDB V3 res/atom names, Parm CDOM_CPLX_rnb_stripped_box.prmtop: Writing 3000 frames (1-Last, 15)
>
> It reads everything except keepext and conect from the input
>
> How can I fix this?
>
> ________________________________________
> From: David A Case <david.case.rutgers.edu>
> Sent: 14 November 2017 03:26 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] pdb snapshots
>
> On Tue, Nov 14, 2017, Lizelle Lubbe wrote:
>>
>> I used the following to create pdb snapshots of my trajectory:
>> trajin filename.nc
>> trajout snapshot.pdb pdb offset 15 multi vdw pdbv3 conect keepext
>>
>> Unfortunately the pdb extension is not kept (files are named
>> snapshot.pdb.1 etc) and the conect records are not written at the end
>
> Which version of cpptraj are you using? (It's printed out at the top of the
> output). Simplest explanation is that you are using old code.
>
> Also, look in the cpptraj output to see if it says anything about arguments
> not being processed.
>
> ....dac
>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Nov 15 2017 - 08:30:02 PST
