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 - 05:00:02 PDT
