[gmx-users] charmm 36 force field for DNA

[Qinghua Liao]

Hello J,

Thanks a lot for your tips, then I can do it manually in minutes. :-)


All the best,
Qinghua

On 09/21/2017 09:09 PM, gromacs query wrote:
> 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.
>
> -J
>
> On Thu, Sep 21, 2017 at 5:23 PM, Qinghua Liao <scorpio.liao at gmail.com>
> wrote:
>
>> 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
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