I have a protein, for which I want to computationally study the effect of its phosphorylation. I was able to add a phosphoryl group to my desired THR residue and the structure looks fine. However, when I try to generate topology using gmx_pdb2gmx, it does not work. I figured it has to do with the extra phosphoryl that i added, which is naturally absent in the aminoacids.rtp file. Hence, I manually created another entry namely "pTHR", where I added the charges for the THR along with the phosphoryl. I tried to generate the topology once again, but its still not accepting it. Kindly tell me if anyone has done it before on gromacs. Thanks, ahead of time.
My phosphothreonine looks like this:
ATOM 2808 N pTHR A 174 231.841 -74.271 -80.471 1.00 0.00 N
ATOM 2809 H pTHR A 174 231.591 -73.451 -81.001 1.00 0.00 H
ATOM 2810 CA pTHR A 174 231.141 -75.531 -80.731 1.00 0.00 C
ATOM 2811 HA pTHR A 174 230.571 -75.901 -79.881 1.00 0.00 H
ATOM 2812 CB pTHR A 174 230.081 -75.331 -81.901 1.00 0.00 C
ATOM 2813 HB pTHR A 174 230.651 -75.081 -82.791 1.00 0.00 H
ATOM 2814 CG2pTHR A 174 229.231 -76.511 -82.181 1.00 0.00 C
ATOM 2815 1HG2pTHR A 174 228.451 -76.411 -82.951 1.00 0.00 H
ATOM 2816 2HG2pTHR A 174 229.861 -77.351 -82.471 1.00 0.00 H
ATOM 2817 3HG2pTHR A 174 228.771 -76.881 -81.261 1.00 0.00 H
ATOM 2818 OG1pTHR A 174 229.141 -74.291 -81.511 1.00 0.00 O
ATOM 2819 C pTHR A 174 232.111 -76.601 -81.201 1.00 0.00 C
ATOM 2820 O pTHR A 174 232.911 -76.371 -82.101 1.00 0.00 O
ATOM 2821 P pTHR A 174 227.940 -74.052 -82.816 1.00 0.00 P
ATOM 2822 O1 pTHR A 174 227.269 -72.653 -82.656 1.00 0.00 O
ATOM 2823 O2 pTHR A 174 228.744 -74.140 -84.379 1.00 0.00 O
ATOM 2824 O3 pTHR A 174 226.709 -75.306 -82.719 1.00 0.00 O
Which FF you are using?
Nowadays, Forcefields inherently supports the phosphorylation of various reisudes, you donot need to add them.
You can read further on this one here:
https://www.researchgate.net/post/Can-someone-recommend-a-MD-force-field-for-phosphorylated-serines
For adding your desired residue, you need to follow steps outlined here:
https://manual.gromacs.org/current/how-to/topology.html
Just a quick fix, instead of using pTHR, just name it to THX or some 3 digit letter, alongwith follow the steps of how to add residue in a forece field.
Thank you for the suggestions. I primarily use amberff99sb for my simulations. I had no idea it can be done using FFs instead of manually adding them. Thank you sharing the useful materials. I will follow through it.
Also, I was able to pass through the topology generation by specifying the three letter phosphoryl name as given by the DSV, and after some time of running, it still seems fine. So I am hoping its fine. Will anyways try to do it as suggested.
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