The developers should be reading this, and I expect will chime in
eventually.
On 5/15/17 4:56 AM, julian.zachmann selvita.home.pl wrote:
> 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 - 12:00:02 PDT
