[gmx-users] NMR restrained MD

[Justin Lemkul]

On 9/11/13 9:57 AM, Rama Krishna Koppisetti wrote:
> Hi Justin,
>
> These type of dihedrals I'm using now,  Is it correct format.
>
>
> [ dihedral
> s
> ]
> ; GROMOS improper dihedrals
> ;  ai   aj   ak   al  funct   angle     fc
>   LH1   LOS   LC2  LC2    2     35.26   334.72
>    LC   LOS   LO   LP2    2      0.00   167.36
>    LC   LOS   LO   LP2    2      0.00   167.36
> [ dihedral
> s
> ]
> ;  ai   aj   ak      al  funct    ph0       cLP   mult
>    LC3   LNL   LH2   LC2    1      0.00     3.77    3
>    LNL   LH2   LC2   LOS    1    180.00     5.86    1
>    LH2   LC2   LOS    LP    1      0.00     3.77    3
>    LC2   LOS    LP   LOS    1      0.00     3.19    3
>     LP   LOS   LC2   LH1    1      0.00     3.77    3
>    LOS   LC2   LH1   LC2    1      0.00     5.92    3
>    LC2   LH1   LOS    LC    1      0.00     3.77    3
>

Aside from the random line breaks that I assume are simply from email line 
wrapping, yes, these are syntactically correct entries for periodic dihedrals 
and thus are not related to the errors shown in the previous post.  Can you 
please answer the question I asked in my last message?  This thread is jumping 
around quite a lot and it is hard to continue providing useful help if posts are 
going in multiple directions.

-Justin

>
> T
> hanks
> Rama
>
>
> On Wed, Sep 11, 2013 at 8:17 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 9/11/13 9:05 AM, Rama Krishna Koppisetti wrote:
>>
>>> Hi Justin,
>>>
>>> Should I use R-B dihedrals for DMPC lipids rather  than periodic
>>> dihedrals.
>>>
>>>
>> You should use whatever the force field tells you.
>>
>>
>>   I'm getting an Error message like,
>>>
>>> ERROR 18815 [file topol.top, line 54180]:
>>>     No default Ryckaert-Bell. types
>>>
>>>
>>> ERROR 18816 [file topol.top, line 54181]:
>>>     No default Ryckaert-Bell. types
>>>
>>>
>> What are the dihedrals on these lines?
>>
>>
>> -Justin
>>
>> --
>> ==============================**====================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
>> 706-7441
>>
>> ==============================**====================
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>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================