[gmx-users] constraining multiple types of bonds

[tarak karmakar]

Thanks Justin
If I want to constrain all the bonds in the substrate molecule present
inside the enzyme cavity then along with SHAKE what I need to use ?




On Fri, Nov 9, 2012 at 5:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 11/8/12 11:36 PM, tarak karmakar wrote:
>>
>> Thanks Justin
>> As you see in the .mdp file I have used SHAKE. So if I want to fix
>> some C-C or C-O then what algorithm I have to use ?
>>
>
> It still doesn't make sense to me why you want to constrain only a subset of
> the bonds in the system.  Please explain.
>
>
>> In my topology file I have specified following bonds to be
>> constrained. The first two are covalent and the last one is M-L
>> non-covalent bond.
>>
>> [ constraints ]
>> ;  index1  index2   funct          length(nm)
>>      6062   6063       1        0.11490000000
>>      6062   6064       1        0.11490000000
>>      6060   4309       1        0.21000000000
>> Now while implementing SHAKE it is showing
>>
>
> This may be the source of your error.  Without an explanation to the above
> point, it is hard to suggest a fix.  For the metal-ligand interaction, I
> have already suggested two alternative approaches.
>
>
>> Program mdrun, VERSION 4.5.5
>> Source code file: invblock.c, line: 79
>>
>> Fatal error:
>> Double entries in block structure. Item 5247 is in blocks 1371 and 1370
>>    Cannot make an unambiguous inverse block.
>>
>> Please suggest me the exact protocol.
>
>
> Please answer the above point, which I inquired about previously.
>
> -Justin
>
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809