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

[James Starlight]

Justin,

with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2
rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp

NOTE 1 [file ./mdps/em.mdp]:
  For energy conservation with switch/shift potentials, rlist should be 0.1
  to 0.3 nm larger than rvdw.

NOTE 2 [file ./mdps/em.mdp]:
  The sum of the two largest charge group radii (0.078024) is larger than
  rlist (1.200000) - rvdw (1.200000)


Should I increase Rlist to the 1.4 ( as well as rcoulomb to the same
value because of PME) ?

2012/12/7, Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>>>
>>> ========================================
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> * Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>
> --
> ========================================
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>