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

[James Starlight]

Justin,

following to your advise I've tried to use charmm 27 ff for simulation
of my protein-cGMP complex ( ligand was parametrized by Swiss Param
server).

Could you provide me with the cut-offs for vdw as well as
electrostatics suitable for simulation in charmm27 and 36 force
fields?

Does anybody know another servers for parametrization of the ligands
for charmm simulation in gromacs?

2012/12/7, Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>
> --
> ========================================
>
> 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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