[gmx-users] charmm 36 force field for DNA

gromacs query gromacsquery at gmail.com
Thu Sep 21 21:09:26 CEST 2017

Hi Qinghua,

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>

> Hello,
> 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,
> Qinghua
> --
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list