query regarding running simulation using AMBER99SSB-ILDN force field

User discussions
1

Dear Gromacs users,

I am trying to perform a simulation for a protein-DNA system using GROMACS 2019 and I want to use AMBER99SB-ILDN force field. I added -NH2 to the C-terminal end of peptide. I checked aminoacids.rtp file and -NH2 option is also present. I was using pdb2gmx for generating topology and parameter file. Please see the command below:

gmx pdb2gmx -f test.pdb -o test.gro -ignh

I did not use -ter flag, as AMBER force field is not compatible with -ter option. But, pdb2gmx converted amidated C-terminus to standard C-terminus (-COO).

I am bit confused regarding this issue. Any kind of advice/ suggestions will be deeply appreciated.

Thanks in advance,
Snehasis Chatterjee

2

Hi Snehasis,

In amber you would add these as additional terminal resiudes ACE, NME, NHE or NH2.
So, in your case it might help giving the added NH2 group an extra residue name and number.

3

BS"D

Based on the command you provided, you don’t seem to have specified the AMBER force field
(or did you choose it interactively?).

Harry

4

Hi Harry,

I specified force field interactively.

Snehasis

5

Hi

Thank you so much for your help. In my protein, terminal residue is SER. I just specified added NH2 group as separate residue name (mentioned in the aminoacids.rtp) . But, residue number is same. It looks, my problem is solved now.

Snehasis