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 - 08:00:02 PDT
