Start here:

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

Hi, 

If I get this correctly - you have the parameters of the base pairs you want to simulate and now you want to conduct a simulation of your system. 

So the problem, if there is one - appears to be you trying to merge the new parameters with the ones you already have from the program's force field (which you said you are using CHARMM36). Which program are you using? - if you use NAMD - all you have to do is to stream the files in order. If you have properly formatted the parameters with the correct atom types - all you need to do is to read the force field files - and once they are in, use the "stream" command to add to those your parameter files. You stream as many files as you want.

Similarly if you use CHARMM instead of NAMD, you would need to use the append command to append to the parameter card your parameters. 

Keep in mind that if the atom types are identical to others in the forcefield files you will overwrite them with your values. So make sure that your values are either correct or unique so that either you don't overwrite or, if you do end up over writing, doing them with correct values. 

Hope this helps. 

Best,

/A

Ashar,

The main problem lies in joining the unnatural DNA bases with the existing DNA natural base parameters. I'm using NAMD. My unnatural base is not a individual molecule. It needs to be attached with the Original DNA sugar phosphate backbone and here lies the problem. It seems that I need to manually edit and add the new PRESidues etc. Please show some more light.

Justin Lemkul Sir,

                            I'm using NAMD with CHARMM force fields. Please tell me how do I mannually edit the CHARMM topology and parameter files. I'm not familiar with gromacs.

You can define your residue as a new RESI entry in the .rtf or .str file when building the PSF.  It's the same approach I mentioned above (for some reason I thought you were talking about Gromacs, so my apologies and you can ignore that).

Hey, 

There is a difference between PRES and RESI. You need to understand in the structure of the DNA nothing is attracted but the bonding is physically maintained by DNA back bone. What this means is that e.g. a ADEnine would be read from the PDB using the identifier as ADE. Depending on if its the first or the last residue in the chain - a PATCH may or may not be applied to it depending on what sort of chemistry you want it to exhibit. The patch comes as PRES. If ADE exists from the second to N-1 position which means the second last - it will have a certain number of ATOMS associated with it in the force field. Now at this stage you need to understand the difference between topology and parameter. 

RESI definitions are there to pick up molecules and build structure files called PSF files with NAMD. These files have now associated the atoms of the molecule with certain atom types. Parameters that dictate the behavior of these atom types are present in the par/prm file associated with NAMD. 

So, two different things. The parameters help the simulation engine (NAMD) control the behavior (depending on the forcefield function). Now - you said you had already determined the parameters, which is only possible once you have gone through everything and should now have the topology of you molecule defined in a file, the format of which is identical to the one of forcefield version 36. Same for the parameter. All you have to do - is to stream the files once you have read the normal v36 parameter file in the NAMD/CONF file.

Hope this helps.

Best,

/A

p.s. If this isn't your answer, then you perhaps need to rephrase your question and provide more information. Good Luck. 

Dear Sirs,

I'm defining my problem precisely again. My molecule is an unnatural base terminated by methyl group from sugar-phosphate backbone I have calculated an initial set of parameters with basic level of validation for my residue. Now I want to link my molecule with backbone again. The sugar and phosphate part is parametrized in CHARMM. It seems that I need to manually edit the topology and parameter files of CHARMM to link my unnatural base with sugar-phosphate backbone. This is the problem troubling me most.