Hi,
I think the keywords are working, but for some reason the warnings are
still printed. The important thing is to check what cpptraj is using
in the output. For example:
```
spam peaks.xyz name SPAM cut 12.0 info spam.info out spam.dat reorder
summary summary.dat dgbulk -40.300 dhbulk -25.200
Warning: 'dgbulk' not specified; using default for SPC/E water.
Warning: 'dhbulk' not specified; using default for SPC/E water.
SPAM:
Solvent [WAT] density peaks taken from peaks.xyz.
120 density peaks will be analyzed from peaks.xyz.
Occupation information printed to spam.info.
Sites are boxes with edge length 1.250
Re-ordering trajectory so each site always has the same water molecule.
Using a non-bonded cutoff of 12.00 Ang. with a EEL shifting function.
Bulk solvent SPAM free energy: -40.300 kcal/mol
Bulk solvent SPAM enthalpy: -25.200 kcal/mol
```
Note that the 'Bulk solvent' values reported are the same as those
specified even though the warning triggered. If in your output these
values do not end up being what you set let me know.
Thanks for the report.
-Dan
On Tue, May 16, 2017 at 11:40 AM, julian.zachmann selvita.home.pl
<julian.zachmann.selvita.home.pl> wrote:
> I am using cpptraj that is included in Amber-17 and the command as shown below
> which is not working:
>
> spam peaks.xyz solv SOL dgbulk -28.4597 dhbulk -17.7415 temperature 300 reorder
> summary spam.out
>
>
>> On May 16, 2017 at 5:19 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>>
>> On Tue, May 16, 2017 at 11:09 AM, julian.zachmann selvita.home.pl
>> <julian.zachmann.selvita.home.pl> wrote:
>> > Hello Dan,
>> >
>> > Thank you for your answer! I had no problem to calculate the values of
>> > dgbulk
>> > and dhbulk.
>> > I calculated them as -28.4597 and -17.7415. Now I have the problem to
>> > include
>> > the values into my SPAM calculation.
>>
>> The keywords are 'dgbulk' and 'dhbulk' (see below). If you use the
>> latest version of cpptraj they should work fine. Hope this helps,
>>
>> -Dan
>>
>> <dgbulk> SPAM free energy of the bulk solvent in kcal/mol; default is
>> -30.3 kcal/mol (SPC/E water).
>> <dhbulk> SPAM enthalpy of the bulk solvent in kcal/mol; default is
>> -22.2 kcal/mol (SPC/E water).
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>>
>> _______________________________________________
>> 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
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 16 2017 - 09:30:03 PDT
