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

[Justin Lemkul]

On 12/7/12 1:19 PM, James Starlight wrote:
> 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?
>

http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html

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

If Google can't find it, it probably doesn't exist.

-Justin

> 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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-- 
========================================

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

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