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

Thu Dec 6 14:53:42 CET 2012

On 12/6/12 2:39 AM, James Starlight wrote:
> Justin,
>
> 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
> program.
>

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 is 
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 good, 
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 parameterization.

-Justin

> [ 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
>
>
>
> James
>
> 2012/12/5 Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>> On 12/5/12 1:39 PM, James Starlight wrote:
>>>
>>> Justin,
>>>
>>> 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 just
>> a recent one.  If you're choosing a force field because it makes life easy,
>> be prepared to defend your results if they are of poor quality or defend a
>> 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 suggest
>> 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
>>> assignment?
>>>
>>
>> That depends on the functional group.  If it's also found in proteins, yes.
>> If not, then maybe but probably not.
>>
>>
>> -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

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