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 - 03:30:02 PDT
