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 - 04:30:02 PDT
