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 - 03:30:03 PDT
