[gmx-users] NADPH parameters

Mark Abraham mark.abraham at anu.edu.au
Sun Mar 27 09:30:46 CEST 2011

On 27/03/11, Kishore  <kris.vempali at gmail.com> wrote:
> Dear Mark/Justin,

You were asked yesterday to do things when you reply to digest emails. Do change the subject to something useful, and do not include the entire digest in your email. Not taking actions to play nicely with the other children will lead to the other children not playing with you :-)

> Thanks for your suggestions. I think I now have a good understanding of what you are talking about. Please answer my one last query in connection with this. Can the NADPH molecule from the starting PDB file be made to comply with the entry for NADPH in Gromacs In built resiude topology file [ NDPP ]. The problem I see in this is that this topology had the explicit polar hydrogens which we do not have in the starting PDB file and even after renaming the atom names and the residue names in the PDB to match with this in built topologies it clearly gives a warning about the missing polar hydrogens. How does one use these inbuilt topologies? What is adviced in this case- Generate topologies some where else (like PRODRG and do the necessary fine tuning) and use them? (or) Can it be made to comply with the in built topology in someway? and finally can the same charges/charge groups as that of the inbuilt topology be assigned to the PRODRG topologies in hope any better better behavior of the system?

First, choose a force field. This will be either all-atom or united-atom. Then, if your input structure for NADPH does not match the .rtp entry (e.g. lacking hydrogen atoms) you have various options. You can build them in with a molecule builder, possibly editing the atom names as suitable. You can use the GROMACS hydrogen database in pdb2gmx to build them (but you may need to write the database entries for NADPH if they are missing - see chapter 5 of the manual). You can generate a structure from scratch that matches, using some external tool. The GROMACS "protonate" tool might be useful.

I would make an effort to determine where the .rtp NADPH parameters came from - hopefully it's documented in the .rtp file, or elsewhere in the force field files. Search the literature for that force field and NADPH, etc. You may then learn what they are known to be useful for.

I would ignore anything PRODRG produced if I had any viable alternative.

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