I believe this could be a bug since it is a new feature.
Can I report this somehow as a possible bug to developers?
> On May 15, 2017 at 1:47 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>
> Maybe you've hit a bug. In any case, deeper than a non-user look can solve.
>
>
> On 5/15/17 4:27 AM, julian.zachmann selvita.home.pl wrote:
> > I have run volmap before. Volmap output is the peaks.xyz file in
> > spam peaks.xyz solv SOL dgbulk -28.4597 dhbulk -17.7415 temperature 300
> > reorder
> > summary spam.out
> >
> > Also all options are in the order as in the manual and everything is on one
> > line.
> > But still I get:
> > Warning: 'dgbulk' not specified; using default for SPC/E water.
> > Warning: 'dhbulk' not specified; using default for SPC/E water.
> >
> >> On May 15, 2017 at 12:22 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
> >>
> >>
> >> Possibly relevant:
> >>
> >> " Prior to this command, the volmap command should be run with the
> >> peakfile keyword (see 28.9.81 on page 646) to generate the peaks file.
> >> If not using peaks from the volmap command, the peaks file should have
> >> one line per peak with format:..."
> >>
> >>
> >> On 5/15/17 3:16 AM, Bill Ross wrote:
> >>> I see it in http://ambermd.org/doc12/Amber17.pdf
> >>>
> >>> You might try ordering the options as in the manual. Maybe put them all
> >>> on one line.
> >>>
> >>>
> >>> On 5/15/17 2:54 AM, Bill Ross wrote:
> >>>> Which manual? I don't see it in
> >>>>
> >>>> http://ambermd.org/doc12/Amber16.pdf
> >>>>
> >>>>
> >>>> On 5/15/17 2:20 AM, julian.zachmann selvita.home.pl wrote:
> >>>>> I have read the manual very carefully.
> >>>>> It could be that I misunderstand something but I really don't see what
> >>>>> it
> >>>>> could
> >>>>> be.
> >>>>> In the manual SPAM is on page 639.
> >>>>>
> >>>>>> On May 15, 2017 at 11:09 AM Bill Ross <ross.cgl.ucsf.edu> wrote:
> >>>>>>
> >>>>>>
> >>>>>> I suspect a careful reading of the manual will indicate that your
> >>>>>> 'spam'
> >>>>>> arguments are incorrect.
> >>>>>>
> >>>>>> Bill
> >>>>>>
> >>>>>>
> >>>>>> On 5/15/17 1:55 AM, julian.zachmann selvita.home.pl wrote:
> >>>>>>> Could anybody please answer me on this?
> >>>>>>>
> >>>>>>>> On May 11, 2017 at 4:29 PM "julian.zachmann selvita.home.pl"
> >>>>>>>> <julian.zachmann.selvita.home.pl> wrote:
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> Hello everybody,
> >>>>>>>>
> >>>>>>>> I have run a md-simulation with Gromacs and want to analysis it now
> >>>>>>>> in
> >>>>>>>> cpptraj
> >>>>>>>> with SPAM. Therefore I use these commands:
> >>>>>>>>
> >>>>>>>> parm 2lyo.prmtop
> >>>>>>>>
> >>>>>>>> trajin 2lyo.trr
> >>>>>>>>
> >>>>>>>> spam peaks.xyz solv SOL reorder dgbulk -28.4597 dhbulk -17.7415
> >>>>>>>> temperature
> >>>>>>>> 300
> >>>>>>>> name 2lyo summary spam.out
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> But I get:
> >>>>>>>>
> >>>>>>>> Warning: 'dgbulk' not specified; using default for SPC/E water.
> >>>>>>>> Warning: 'dhbulk' not specified; using default for SPC/E water.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>> Could somebody please indicate me how I can correctly set dgbulk and
> >>>>>>>> dhbulk
> >>>>>>>> for
> >>>>>>>> my water model tip3p.
> >>>>>>>>
> >>>>>>>> Thank you very much and best regards!
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Received on Mon May 15 2017 - 05:00:03 PDT
