[gmx-users] CNT force field and simulation

[Alex]

Hi Pierre,

Two things:

1. rtp entries are pretty useless for crystal structures. Biochemical
simulations use molecules with a precise atomic composition, so an rtp
template makes sense. Not for crystals. Your rtp entry contains useless
information and the only thing in your coordinates that can fit that
template is one atom, which is already generous. So, you get one atom in
your GRO. ;)

2. Andrea isn't using pdb2gmx, which relies on templates. I honestly have
no idea why he created that rtp entry, so maybe other users will clarify
that. Andrea uses x2top, which will look up data in ffbonded, ffnonbonded,
and in atomname to type translator. This is the right way to treat crystals
in GMX. Moreover, you will have to do that every time you have a new set of
coordinates. Use what he uses and you won't get any new GRO files. All you
will get is a topology to go with your original PDB -- and that is all you
need to run a simulation.

Alex




On Mon, Apr 13, 2015 at 5:49 PM, Pierre Bertin <bertinp71 at gmail.com> wrote:

> Hi Alex,
>
> All right, I red all this weekend and I know how to modify a force field
> to add residues (I hope... ahah). I modified OPLSAA force field because I
> want to add a protein to my CNT.
>
> So, I have edited these files with Andrea Minoia datas (and yours) :
>
> *aminoacids.rtp* :
>
> [ CNT ]
>
>   39  [ atoms ]
>
>   40      SWT    SWT    0     2
>
>   41      SWT    SWT    0     3
>
>   42  [ bonds ]
>
>   43    SWT  SWT  SWT
>
>
>   44    SWT  SWT
>
> I added a new residue named CNT. 2 or 3 bonds, I do not include hydrogen
> to start. So a carbon can have 2 (extremities) or 3 bonds (internal).
>
>
>
> *atomname2type.n2t :*
>
>  24 C    SWT         0      12.011  2    SWT 0.142   SWT 0.142
>
>  25 C    SWT         0      12.011  3    SWT 0.142   SWT 0.142   SWT 0.142
>
> Here, conversion of C atoms from CNT.pdb file to SWT new atom type.
>
>
> *atomtypes.atp :*
>
> 823  SWT        12.01100  ;CNT
>
> Here, define the new atom type : SWT with the carbon mass.
>
>
> *ffbonded.itp : *
>
> [ bonds ]
>
> SWT   SWT     1    0.1420    420420.0   ; CNT
> ​SWT SWT bond is a bond between 2 carbons in CNT. I have used your data
> Alex. ​
>
> [ angletype ]
>
> SWT    SWT    SWT     1   120.000    659.346   ; CNT
> Angle type between the 3 atoms of carbon with datas from you email and the
> same in dihedral with :
>
> [ dihedraltypes ]
>
> SWT    SWT    SWT    SWT     3     17.30770   0.00000 -17.30770   0.00000
>   0.00000   0.00000      ; CNT
>
> ​I have tried with SWT, with C and in n2t with a reference to oplsaa
> carbon from benzene.
>
> This works, I can build the .gro file with :
> gmx pdb2gmx -f cnt_gro.pdb -o cnt_gro.gro -p cnt_gro.top
> And then I select OPLSAA force field and TIP3P for water.
>
> Problem : My cnt_gro.gro has only ONE atom of carbon. And I do not have
> error message. What did I do wrong?
>
> Thanks you a lot for your consideration and time. I attach the pdb file. ​
>
>
>
>
> *Pierre BERTIN*
> Bioinformatics and Biostatistics student (MSc),
> University Paris-Sud XI, ORSAY.
>
>
> 2015-04-11 14:31 GMT-06:00 Alex <nedomacho at gmail.com>:
>
>>  Great, glad it's working.
>>
>>
>> I think there was a wrong bond length somewhere in Andrea's tutorial, not
>> sure where exactly (I could be wrong). Look at everything carefully and
>> make sure the bond lengths are at 0.142 nm, because this is what the
>> generator is doing.
>>
>>
>> Have fun!
>>
>>
>> Alex
>>
>>
>>
>>   >
>>
>> ​Thank you a lot, I did this and exactly as you are saying I do not have
>> the message.
>>
>>
>> I use the link posted in my first message : ​(
>> http://www.nanotube.msu.edu/tubeASP/)
>>
>> And then, I converted with Babel.
>>
>>
>> But I removed CONECT statements. And now I am modifying files as you said
>> and trying to run the tutorial.
>>
>>
>> Thank you a lot Alex!
>>
>>
>>
>>
>>
>>
>>
>>
>