I think you can use 'restraintmask' for restraining all the heavy
atoms, then use GROUP syntax for the rest of your restraints.
-Dan
On Mon, Apr 11, 2016 at 12:56 PM, Stevens, David Ryan
<drsteve2.illinois.edu> wrote:
> Hi Dan,
>
> But what about the two different restraints? How do I add my other restraints on top?
>
> Example?? - Because this does not work. It only works for one restraint variable.
> ntr=1
> restraintmask=‘:1-150!.H= :1.O2’,H2’ :2.OP2’
> restraint_wt=10.0, 100.0
>
> Thanks,
>
> David
>
>
>
>
> On 4/11/16, 12:08 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
>
>>To restrain everything but hydrogen it's probably easier to use the
>>'restraintmask'/'ntr'/'restraint_wt' namelist variables (use mask
>>'!.H='), then add your other restraints on top.
>>
>>-Dan
>>
>>On Mon, Apr 11, 2016 at 10:03 AM, Stevens, David Ryan
>><drsteve2.illinois.edu> wrote:
>>> Hi,
>>>
>>> I want to use multiple restraints for my system during minimization. I want to restrain everything but the hydrogens as part of my minimization, but I also want to maintain a different set of restraints for a different set of atoms (on top of the hydrogen restraints). Is there a better way to do this?
>>>
>>> Upon seeing a reply regarding a similar issue in the archives from 2009, I worked through the GROUP input example in the AMBER9 Manual (Appendix B). I tried doing this, but I couldn’t compose the mask correctly for everything but the hydrogens.
>>>
>>> Title one
>>> 10.0 #force constant
>>> FIND
>>> **!.H* <- This is the syntax that I am struggling with
>>> RES 1 150
>>> END
>>> Title two
>>> 100.0 #force constant
>>> ATOM 29 30
>>> END
>>> Title three
>>> 100.0 #force constant
>>> ATOM 30 34
>>> END
>>> END
>>>
>>> Thank you,
>>>
>>> David Stevens
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>--
>>-------------------------
>>Daniel R. Roe, PhD
>>Department of Medicinal Chemistry
>>University of Utah
>>30 South 2000 East, Room 307
>>Salt Lake City, UT 84112-5820
>>http://home.chpc.utah.edu/~cheatham/
>>(801) 587-9652
>>(801) 585-6208 (Fax)
>>
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>>AMBER mailing list
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>>http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Apr 11 2016 - 13:00:03 PDT
