How can I build caps of the amino acid residues of my peptide (downloaded from RCSB) so as to incorporate into GROMACS?

07 July 2016 7 8K Report

I want to cap the ends of my peptide chain. Though -ter option of pdb2gmx takes up its zwitterionic form quite easily, I've read somewhere that termini are quite mobile and it is better to proceed with capping. I want to use GROMOS53a6 parameters and I've found entries of ACE and NAC in its .rtp file. My dilemma is how to build caps onto my pdb file? What about their coordinates? Where should I insert them? I tried building it using pymol but it didn't work. Some softwares like Schrodinger's Protein Preparation Wzard is great with stuff like this but I don't have the resources to buy paid software. Could you please suggest a way how to do this?

Here are some of the coordinates

Starting residue:

ATOM 1 N GLN A 1 7.066 21.384 0.641 1.00 11.02 N

ATOM 2 CA GLN A 1 5.949 20.973 1.534 1.00 10.36 C

ATOM 3 C GLN A 1 5.275 19.686 1.047 1.00 9.45 C

ATOM 4 O GLN A 1 5.014 18.782 1.840 1.00 9.34 O

ATOM 5 CB GLN A 1 4.928 22.115 1.616 1.00 10.69 C

ATOM 6 CG GLN A 1 3.676 21.765 2.403 1.00 11.26 C

ATOM 7 CD GLN A 1 3.987 21.223 3.784 1.00 11.68 C

ATOM 8 OE1 GLN A 1 3.745 20.021 4.019 1.00 11.97 O

ATOM 9 NE2 GLN A 1 4.475 22.002 4.632 1.00 11.90 N

ATOM 10 H1 GLN A 1 7.823 21.771 1.239 1.00 11.21 H

ATOM 11 H2 GLN A 1 6.702 22.105 -0.016 1.00 11.26 H

ATOM 12 H3 GLN A 1 7.392 20.540 0.130 1.00 11.19 H

ATOM 13 HA GLN A 1 6.354 20.797 2.521 1.00 10.53 H

ATOM 14 HB2 GLN A 1 5.397 22.965 2.088 1.00 10.93 H

ATOM 15 HB3 GLN A 1 4.631 22.391 0.615 1.00 10.52 H

ATOM 16 HG2 GLN A 1 3.073 22.656 2.510 1.00 11.34 H

ATOM 17 HG3 GLN A 1 3.119 21.019 1.857 1.00 11.54 H

Ending residue

ATOM 475 N LEU A 33 -9.783 -18.497 -1.487 1.00 5.97 N

ATOM 476 CA LEU A 33 -10.736 -19.453 -0.936 1.00 6.85 C

ATOM 477 C LEU A 33 -10.018 -20.571 -0.187 1.00 7.51 C

ATOM 478 O LEU A 33 -10.708 -21.452 0.366 1.00 7.81 O

ATOM 479 CB LEU A 33 -11.601 -20.043 -2.052 1.00 7.27 C

ATOM 480 CG LEU A 33 -12.071 -19.040 -3.107 1.00 7.87 C

ATOM 481 CD1 LEU A 33 -12.991 -19.715 -4.113 1.00 8.08 C

ATOM 482 CD2 LEU A 33 -12.773 -17.862 -2.446 1.00 8.48 C

ATOM 483 OXT LEU A 33 -8.769 -20.557 -0.163 1.00 7.98 O

ATOM 484 H LEU A 33 -9.837 -17.556 -1.214 1.00 5.99 H

ATOM 485 HA LEU A 33 -11.373 -18.923 -0.242 1.00 7.08 H

ATOM 486 HB2 LEU A 33 -11.031 -20.815 -2.548 1.00 7.07 H

ATOM 487 HB3 LEU A 33 -12.473 -20.495 -1.604 1.00 7.69 H

ATOM 488 HG LEU A 33 -11.213 -18.661 -3.642 1.00 8.04 H

ATOM 489 HD11 LEU A 33 -12.516 -20.606 -4.494 1.00 8.27 H

ATOM 490 HD12 LEU A 33 -13.192 -19.036 -4.928 1.00 8.16 H

ATOM 491 HD13 LEU A 33 -13.920 -19.979 -3.629 1.00 8.27 H

ATOM 492 HD21 LEU A 33 -12.052 -17.087 -2.232 1.00 8.84 H

ATOM 493 HD22 LEU A 33 -13.234 -18.189 -1.527 1.00 8.47 H

ATOM 494 HD23 LEU A 33 -13.531 -17.476 -3.112 1.00 8.84 H

Tristan Croll

It's been quite some time since I've used GROMACS, but if I recall correctly you can do this in pdb2gmx. Including the -ter flag at the command line should bring up dialogues during processing to allow you to choose different termini (it will choose coordinates for the new atoms automatically).

Apramita Chand

Thanks for your reply, Tristan

Actually, -ter command does not provide an option for capping. It asks you to choose from options like -NH2 or NH3+ and -COOH or COO- respectively. What I want to do is to add caps at the end of the peptide chain . Any suggestions on how to go about it?

Apramita Chand

Dear Martin,

Usually, I can build short peptides through build residue option in PYMOL.I tried to add residue ACE onto the end of my peptide chain by selecting N atom and it's adding somewhere else but not where I need it. I tried removing hydrogens and adding and various other ways but I can't seem to be able to get it done. If you know how to add it to a peptide(pdb downloaded from data bank), in pymol ,please guide me through the steps.

Martin Klvana

To add the acetyl group to the N-terminal backbone nitrogen atom in PyMOL (v. 0.99rc6):

1. Select the nitrogen: .

2. Add acetyl group to the nitrogen: Menu >>> Build >>> Residue >>> Acetyl.

3. If you need to adjust the torsion angle(s), it can also be done in PyMOL:

http://www.pymolwiki.org/index.php/Torsion

Ishrat Jahan

Hello Martin,

I have done capping in pymol but when i run its pdb2gmx, an error occured says residue type NME not found in .rtp file.

will you please tell me what to do?

Martin Klvana

Add the "NME" residue into the residue topology (rtp) file.

http://manual.gromacs.org/online/rtp.html

---

Not a Gromacs user.

How to incorporate the KBFF urea model into a force field in GROMACS package?

How do you define inter-peptide and intra-peptide contacts/hydrogen bonds in a multiple peptide simulation?

How to implement specific solute models in GROMACS force fields?

How to calculate preferential interaction coefficient between protein-water/cosolute from GROMACS trajectory?

Is it possible that short peptides may adopt compact conformation in urea solution and extended form in presence of protecting osmolyte?

Hydrogen Bond Lifetimes calculated in gromacs with and without applying pbc are different. Which value should be considered?

Problem with center-of-mass RDF and subsequent coordination number calculation in GROMACS

What is the correct way of calculating hydrogen bond lifetime in GROMACS?

Is there any way of calculating hydrogen bond energy in GROMACS?

Correct way of calculating diffusion constant through velocity autocorrelation in GROMACS

error in running a model in Abaqus

error in modelling model in Abaqus

MD MOE RMSD

MD MOE RMSD

MGL tools

fatal error

fatal error

fatal error

fatal error

flexibility of polymers chain