[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields
jmsstarlight at gmail.com
Thu Dec 6 19:12:19 CET 2012
Thanks again for explanation.
It's interesting that above parametrization made by ATB have cased the
system to crash within first ps of modeling ;) (On the contrarythe
system with the ligand made by prodrg have been very stable during
100ns). I ve tried to re-parametrized my molecule by another algorithm
implemented in ATB ( am1 instead of pm3 which was used in the crashed
2012/12/6, Justin Lemkul <jalemkul at vt.edu>:
> On 12/6/12 2:39 AM, James Starlight wrote:
>> Could you provide me with the example of the server where I could
>> obtain Gromac's itp topologies for the charmm ff? I know many such
>> servers which could be useful only for preparation systems for NAMD
> Google "CHARMM ligand topology in Gromacs" (without the quotes) - the first
> result is what you're looking for.
>> By the way recently I've made parametrization of my cGMP molecule by
>> means of ATB server. In the below example you can see that the charge
>> distribution is differs from the PRODRG example of that molecule which
>> I've posted yesterday. Does that charge distribution more suitable for
>> the 54a force field?
> Given that PRODRG generally produces very bad charges, just about anything
> better ;)
> Nucleotide parameters already exist in 54A7, I don't see why you necessarily
> have to create them from scratch. In general, these charges look pretty
> but note that DGUA already exists and can describe most of your molecule
> already. The cyclic part is the only trick, but the nucleobase parameters
> should be the same in cGMP and DGUA, given the nature of Gromos96
>> [ atoms ]
>> ; nr type resnr resid atom cgnr charge mass total_charge
>> 1 NT 1 _N4H N2 1 -0.832 14.0067
>> 2 H 1 _N4H H22 1 0.416 1.0080
>> 3 H 1 _N4H H21 1 0.416 1.0080 ; 0.000
>> 4 NR 1 _N4H N1 2 -0.715 14.0067
>> 5 H 1 _N4H H1 2 0.427 1.0080
>> 6 C 1 _N4H C2 2 0.775 12.0110
>> 7 NR 1 _N4H N3 2 -0.691 14.0067
>> 8 C 1 _N4H C4 2 0.431 12.0110
>> 9 NR 1 _N4H N9 2 -0.227 14.0067 ; 0.000
>> 10 C 1 _N4H C8 3 0.220 12.0110
>> 11 HC 1 _N4H H01 3 0.162 1.0080
>> 12 O 1 _N4H O6 3 -0.556 15.9994
>> 13 C 1 _N4H C6 3 0.669 12.0110
>> 14 C 1 _N4H C5 3 0.026 12.0110
>> 15 NR 1 _N4H N7 3 -0.521 14.0067 ; 0.000
>> 16 OE 1 _N4H O4* 4 -0.429 15.9994
>> 17 CH1 1 _N4H C1* 4 0.429 13.0190 ; 0.000
>> 18 CH1 1 _N4H C4* 5 0.000 13.0190 ; 0.000
>> 19 OA 1 _N4H O5* 6 -0.422 15.9994
>> 20 P 1 _N4H PAQ 6 0.971 30.9738
>> 21 OM 1 _N4H OAR 6 -0.613 15.9994
>> 22 OA 1 _N4H O3* 6 -0.382 15.9994
>> 23 OA 1 _N4H OAS 6 -0.617 15.9994
>> 24 H 1 _N4H H03 6 0.497 1.0080
>> 25 CH2 1 _N4H C5* 6 0.319 14.0270
>> 26 CH1 1 _N4H C3* 6 0.247 13.0190 ; -0.000
>> 27 CH1 1 _N4H C2* 7 0.200 13.0190
>> 28 OA 1 _N4H O2* 7 -0.614 15.9994
>> 29 H 1 _N4H H8M 7 0.414 1.0080 ; 0.000
>> 2012/12/5 Justin Lemkul <jalemkul at vt.edu>:
>>> On 12/5/12 1:39 PM, James Starlight wrote:
>>>> Indeed the force field is the 54a7 ( modiffied version of the 54a6).
>>>> The main reason of using GROMOS ff in that case was the topology of
>>>> ligands which could be easily created by means of prodrg or ATB. On
>>>> other hand I've never worked with the protein-ligand complexes in
>>>> charmm ff for instance.
>>> Well, you get out what you put in. A recent paper
>>> (dx.doi.org/10.1002/jcc.23055) showed that Gromos force fields performed
>>> very poorly for simulating nucleic acids. There are others, but that's
>>> a recent one. If you're choosing a force field because it makes life
>>> be prepared to defend your results if they are of poor quality or defend
>>> lot of wasted time while you re-do the simulations :)
>>> There are servers that produce CHARMM topologies and other programs that
>>> will convert AMBER topologies into Gromacs format as well. I would
>>> you evaluate all the options available.
>>>> By the way is there any suitable builing blocks (implemented in the
>>>> rtp enties of the gromos ff) which could be used for charge
>>> That depends on the functional group. If it's also found in proteins,
>>> If not, then maybe but probably not.
>>> Justin A. Lemkul, Ph.D.
>>> Research Scientist
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> gmx-users mailing list gmx-users at gromacs.org
>>> * 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
> gmx-users mailing list gmx-users at gromacs.org
> * 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
More information about the gromacs.org_gmx-users