Using APBS with coarse-grained models of proteins

[fabiotrovato]

Dear APBS community,

I would like to know if APBS can be used with coarse-grained protein structures (for example protein models with one pseudo-atom per residue) for which I know the relevant quantities such as pseudo-atom radii and charges. It seems that the PQR file format should be flexible enough to do it. However, I am not sure if during calculation APBS expects to find conventional atoms for each given protein residue.

Any guidance to be able to set up the calculation of the electrostatic potential surface of a generic coarse-grained protein model is highly appreciated.

Thank you and keep up with the good work! Fabio

[sobolevnrm]

Hi Fabio --

Thank you for the suggestion! Can you provide an example of the type of file you'd like to parameterize and more information about the parameter set you'd use?

Thanks,

Nathan

On Fri, May 8, 2020 at 3:52 AM fabiotrovato notifications@github.com wrote:

Dear APBS community,

I would like to know if APBS can be used with coarse-grained protein structures (for example protein models with one pseudo-atom per residue) for which I know the relevant quantities such as pseudo-atom radii and charges. It seems that the PQR file format should be flexible enough to do it. However, I am not sure if during calculation APBS expects to find conventional atoms for each given protein residue.

Any guidance to be able to set up the calculation of the electrostatic potential surface of a generic coarse-grained protein model is highly appreciated.

Thank you and keep up with the good work! Fabio

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Electrostatics/apbs-pdb2pqr/issues/598, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAOX7WGPDIANK7ZMRX6SUUDRQPP7FANCNFSM4M4CP47A .

[fabiotrovato]

Hi Nathan,

Sure, i will try to explain what I would need for my project.

I have a protein sequence of about 1800 residues and we are modelling its tertiary structure. Since it's too big for an atomistic representation, I have coarse-grained it as a polymer of about 600 pseudo-atoms (beads). In some regions, one bead corresponds to one residue, in others it corresponds to three residues. So if the bead represents a Lysine, i assign to it a charge +1 and vdw radius 4 Ang. If the bead represents, say, Lys Lys Ala, I assign to it charge +2 and vdw radius 10 Ang.

With this model protein, i performed molecular dynamics simulations (I parameterized the force field myself). To be more specific, i run Langevin dynamics as I do not have any solvent molecules, just the 600 residue long polypeptide. I got a trajectory and I would like to calculate the electrostatic potential of each conformation.

I can convert each conformation to the appropriate format accepted by APBS. I can assume physiological ionic conditions and so on. Any suggestion is highly appreciated.

Thanks! Fabio

[fabiotrovato]

I guess what I'm asking is whether i can use APBS with my model protein or if I'm gonna get stuck at a certain point (still haven't tried anything so i can't provide an example, sorry)

[fabiotrovato]

Hi Nathan, I'm following up to see if you have any suggestions on this? Thanks, Fabio

[sobolevnrm]

Hello -

What you're describing is definitely possible with APBS. You have enough information to construct the PQR file yourself and can then start directly with APBS using your custom PQR for the coarse-grained protein.

Thanks,

Nathan

On Sat, May 9, 2020 at 9:53 AM fabiotrovato notifications@github.com wrote:

Hi Nathan,

Sure, i will try to explain what I would need for my project.

I have a protein sequence of about 1800 residues and we are modelling its tertiary structure. Since it's too big for an atomistic representation, I have coarse-grained it as a polymer of about 600 pseudo-atoms (beads). In some regions, one bead corresponds to one residue, in others it corresponds to three residues. So if the bead represents a Lysine, i assign to it a charge +1 and vdw radius 4 Ang. If the bead represents, say, Lys Lys Ala, I assign to it charge +2 and vdw radius 10 Ang.

With this model protein, i performed molecular dynamics simulations (I parameterized the force field myself). To be more specific, i run Langevin dynamics as I do not have any solvent molecules, just the 600 residue long polypeptide. I got a trajectory and I would like to calculate the electrostatic potential of each conformation.

I can convert each conformation to the appropriate format accepted by APBS. I can assume physiological ionic conditions and so on. Any suggestion is highly appreciated.

Thanks! Fabio

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Electrostatics/apbs-pdb2pqr/issues/598#issuecomment-626204962, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAOX7WEIP5KORGVIPBYY3VTRQWDARANCNFSM4M4CP47A .

[fabiotrovato]

Hi, thanks for your feedback. I will give this a try. If I manage to do the calculation, should I post the input files here? Might be a guide for someone who needs to do something similar. Best, Fabio

[sobolevnrm]

That would be great; thanks!

On Tue, May 12, 2020 at 6:15 AM fabiotrovato notifications@github.com wrote:

Hi, thanks for your feedback. I will give this a try. If I manage to do the calculation, should I post the input files here? Might be a guide for someone who needs to do something similar. Best, Fabio

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Electrostatics/apbs-pdb2pqr/issues/598#issuecomment-627336805, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAOX7WB4OAMPBQAKAWR5VBTRRFDWBANCNFSM4M4CP47A .