Hello Dan,
Thank you for your answer! I had no problem to calculate the values of dgbulk
and dhbulk.
I calculated them as -28.4597 and -17.7415. Now I have the problem to include
the values into my SPAM calculation.
PS: I am reading the most up to date manual for Amber 17 and do everything as it
is written there!
Best wishes,
Julian
> On May 16, 2017 at 4:49 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>
> Hi,
>
> Make sure you're reading the most up to date manual for Amber 17. The
> relevant text is at the end of the command description:
>
> "Values of dgbulk and dhbulk for different water models can be
> calculated from pure water simulations with the purewater keyword."
>
> You need to run a pure water simulation and analyze it with 'spam
> purewater'. This will help you get the average values. Hope this
> helps,
>
> -Dan
>
> On Mon, May 15, 2017 at 7:27 AM, julian.zachmann selvita.home.pl
> <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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>
> --
> -------------------------
> 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 Tue May 16 2017 - 08:30:03 PDT
