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!
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 15 2017 - 03:00:02 PDT
