[gmx-users] constraining multiple types of bonds
tarak20489 at gmail.com
Sun Nov 11 04:27:32 CET 2012
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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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