Thank you, this worked.
I appreciate your help,
David
On 4/11/16, 2:34 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
>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
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
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>>>> 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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>>>http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
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>> 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)
>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Apr 11 2016 - 14:30:03 PDT
