[gmx-users] charmm 36 force field for DNA
gromacsquery at gmail.com
Thu Sep 21 21:09:26 CEST 2017
I am not sure about any too but If you have pdb working fine with AMBER
(as you said) then its not much of work doing it 'manually' ; takes less
than two minutes. You can do this:
1) First remove hydrogens and let gromacs add by itself at the final step
(matching from charm36). You can use 'sed' to remove pdb lines matching ' H'
2) Then from this pdb replace these 3 atom names (using vi or any text
editor or sed)
Note: You may need to remove 5s and 3s from DA/DT/DC/DG
C7 to C5M (found in DT)
OP1 to O1P (in all bases)
OP2 to O2P (in all bases)
3) Now load this new PDB (Gromacs will add Hs). I hope it works.
On Thu, Sep 21, 2017 at 5:23 PM, Qinghua Liao <scorpio.liao at gmail.com>
> I want to simulate a DNA with CHARMM 36 force field, but I found that the
> atom names in the pdb downloaded from the PDB data bank
> do not match those in the CHARMM 36 force field. Is there a better tool to
> edit it properly than modifying manually? Thanks a lot!
> PS: They match well with Amber force field, I don't need to do any changes.
> All the best,
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