[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

[Justin Lemkul]

On 12/7/12 11:42 AM, James Starlight wrote:
> Justin,
>
> ligand-only simulation in vacuum have been finished with the same errors :)
>
> Step 19200, time 38.4 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.025443, max 0.140660 (between atoms 1 and 3)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>        1      2   52.2    0.1033   0.0985      0.1000
>        1      3   90.1    0.1168   0.1141      0.1000
>
> Step 19200, time 38.4 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.025376, max 0.140474 (between atoms 1 and 3)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>        1      2   52.0    0.1033   0.0988      0.1000
>        1      3   90.0    0.1168   0.1140      0.1000
> step 19200, will finish Sat Dec  8 04:10:49 2012
> Step 19201, time 38.402 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.052715, max 0.293316 (between atoms 1 and 3)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>        1      2   49.3    0.0988   0.0993      0.1000
>        1      3   90.0    0.1140   0.1293      0.1000
>
> Step 19201, time 38.402 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.052900, max 0.294281 (between atoms 1 and 3)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>        1      2   49.6    0.0988   0.0989      0.1000
>        1      3   90.0    0.1140   0.1294      0.1000
>
> Step 19202, time 38.404 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.035783, max 0.198482 (between atoms 1 and 3)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>        1      2   33.3    0.0989   0.0984      0.1000
>        1      3   89.9    0.1294   0.1198      0.1000
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.4
> Source code file: /tmp/gromacs-4.5.4/src/mdlib/constr.c, line: 176
>
> Fatal error:
> Too many LINCS warnings (1000)
>
>
> ITs intresting that the same files (like step-1c_n11.pdb) have been
> produced already during CG minimisation phase but the system have not
> been crashed. So I suppoe that the problem is in geometry of the

If you get errors in the minimization, that should indicate that either the 
topology or configuration is flawed.

> mollecule. The direct comparison of the bonds and angles with the rtp
> (DGUA) is non trivial again because of differs in the file formats
> representation :)
>

Most troubleshooting is not easy.  You can also create a topology for DGUA from 
just about any DNA structure and compare its .top against your cGMP topology.

-Justin

-- 
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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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