(Note: These tutorials are meant to provide
illustrative examples of how to use the AMBER software suite to carry out
simulations that can be run on a simple workstation in a reasonable period of
time. They do not necessarily provide the optimal choice of parameters or
methods for the particular application area.)
Copyright Ross Walker 2008
Building your own Custom Residues (old version) - SECTION 1
By Ross Walker
Stage 1 - Do some editing of the PDB file.
The pdb file we will use is PDB ID: 1PLC - 1PLC.pdb.
You should always read all of the header information in a pdb file since it often contains important information about disordered pairs etc. Often 1 pdb file can also contain a series of different structures / inhibitors etc for the same protein system. In this pdb we see that waters #187 and #183 form a disordered pair and so both should not be present.
REMARK 4 1PLC 83 REMARK 4 HOH 187 AND HOH 183 FORM A DISORDERED PAIR AND BOTH ARE NOT 1PLC 84 REMARK 4 PRESENT SIMULTANEOUSLY. 1PLC 85 |
Thus I will arbitrarily remove water 187 from the pdb file and keep 183. I will also remove all of the connectivity data at the end of the PDB as this will not be used by XLeap. Each of our water molecules here is an individual residue. Normally we need to add TER cards between residues that are not bound together in a chain. Fortunately we don't need to do that for our crystallographic waters since XLeap is smart enough to know that each of our waters is a separate molecule. This is defined in the WAT unit. Note, if you were to use different solvents here, such as chloroform, it would be necessary to add the TER cards.
Since pdb files do not distinguish between cysteine residues that are involved in bonds or other things (and hence which have no proton on the sulphur atom) we need to edit the relevant cysteine residues to correct for this. The residue name used by Leap for regular protonated cysteine residues is CYS, for deprotonated (-ve charge) and/or bound to metal atoms it is CYM and for cysteine residues involved in disulphide bridges and other bonds it is CYX. Since cysteine 84 in plastocyanin is bonded to the copper ion we need to change the residue name of residue 84 from CYS to CYM. The same is true for histidine residues which can be protonated in the 'delta' position (HID), the epsilon position (HIE) or at both (HIP). Fortunately in plastocyanin this is fairly easy since there are only two histidine residues (37 and 87) both of which are bonded to the copper via the 'delta' nitrogen. Thus they must both be protonated on the epsilon nitrogen. We will thus change both histidine residue names (37 and 87) from HIS to HIE. Leap will then add the correct number of protons in the correct positions.
Here is the modified pdb file so far: 1PLC_mod.pdb
The next stage before we can use the PDB is to sort out the non-standard hydrogen names. While it is possible to use protonate to correct the non-standard hydrogen names, converting them from NMR conventions to PDB conventions, experience has shown that hydrogen positions in NMR structures can't always be trusted. The best option therefore is to remove all the protons and allow Leap to add them back in at standard positions. Since we will typically minimise our system before running MD this shouldn't pose any problems.
Here is the pdb with the protons removed: 1PLC_mod2.pdb
The next stage is to work out how we are going to treat the copper atom. For this example we shall keep it simple and just treat the copper as a +1 ion bound to the nearby residues. Ideally we would like to make the 4 copper bound residues new non-standard residues and then re-fit all the charges and parameters for these residues and the copper atom. This is a large amount of work, however, and well beyond the scope of this tutorial. For this reason we shall treat the copper atom as simply as possible. We will thus make the copper atom its own residue called CUA (note: in picking a residue name anything would do as long as it is 3 characters long and not currently in use... You can use the list command in Leap to check what residue names are currently being used.).
So we will edit our pdb file and change the copper residue name to CUA.
ATOM 1538 OD1 ASN 99 7.523 13.716 33.177 1.00 33.45 1PLC1661 ATOM 1539 ND2 ASN 99 8.763 14.800 34.732 1.00 31.51 1PLC1662 ATOM 1540 OXT ASN 99 8.932 10.327 32.908 1.00 32.10 1PLC1663 TER 1547 ASN 99 1PLC1670 HETATM 1548 CU CUA 100 7.050 34.960 18.716 1.00 8.78 1PLC1671 HETATM 1549 O HOH 101 17.504 16.825 14.073 1.00 20.28 1PLC1672 HETATM 1550 O HOH 102 18.877 15.088 18.086 1.00 22.16 1PLC1673 HETATM 1551 O HOH 103 11.165 21.823 31.513 1.00 16.99 1PLC1674 |
The original pdb file also contained several "alternate" configurations for some residues. E.g. for LYS 30 we had
ATOM 426 N LYS 30 -0.930 27.774 20.957 1.00 8.07 1PLC 549 ATOM 427 CA LYS 30 -2.028 28.602 20.421 1.00 10.86 1PLC 550 ATOM 428 C LYS 30 -1.629 30.029 20.254 1.00 9.16 1PLC 551 ATOM 429 O LYS 30 -1.226 30.665 21.243 1.00 7.63 1PLC 552 ATOM 430 CB ALYS 30 -3.201 28.489 21.415 0.50 13.41 1PLC 553 ATOM 431 CB BLYS 30 -3.250 28.517 21.354 0.50 15.09 1PLC 554 ATOM 432 CG ALYS 30 -4.397 29.366 21.249 0.50 16.84 1PLC 555 ATOM 433 CG BLYS 30 -4.600 28.495 20.646 0.50 21.50 1PLC 556 ATOM 434 CD ALYS 30 -5.681 28.891 21.893 0.50 20.64 1PLC 557 ATOM 435 CD BLYS 30 -5.745 28.171 21.589 0.50 24.43 1PLC 558 ATOM 436 CE ALYS 30 -5.527 28.212 23.225 0.50 23.18 1PLC 559 ATOM 437 CE BLYS 30 -5.585 26.973 22.460 0.50 24.88 1PLC 560 ATOM 438 NZ ALYS 30 -6.825 28.052 23.929 0.50 20.02 1PLC 561 ATOM 439 NZ BLYS 30 -5.971 25.681 21.860 0.50 26.52 1PLC 562 ATOM 440 H LYS 30 -0.661 27.945 21.802 1.00 8.96 1PLC 563 ATOM 441 HA LYS 30 -2.302 28.229 19.582 1.00 10.61 1PLC 564 ATOM 442 1HB ALYS 30 -3.380 27.572 21.665 0.50 14.09 1PLC 565 ATOM 443 1HB BLYS 30 -3.134 27.712 21.919 0.50 15.93 1PLC 566 ATOM 444 2HB ALYS 30 -2.700 28.880 22.297 0.50 13.96 1PLC 567 ATOM 445 2HB BLYS 30 -3.188 29.326 21.939 0.50 15.16 1PLC 568 ATOM 446 1HG ALYS 30 -4.210 30.316 21.598 0.50 18.44 1PLC 569 ATOM 447 1HG BLYS 30 -4.784 29.428 20.234 0.50 20.74 1PLC 570 ATOM 448 2HG ALYS 30 -4.609 29.538 20.265 0.50 17.98 1PLC 571 ATOM 449 2HG BLYS 30 -4.629 27.910 19.855 0.50 20.04 1PLC 572 ATOM 450 1HD ALYS 30 -6.278 29.712 22.058 0.50 21.47 1PLC 573 ATOM 451 1HD BLYS 30 -5.929 28.976 22.170 0.50 24.46 1PLC 574 ATOM 452 2HD ALYS 30 -6.224 28.346 21.263 0.50 21.94 1PLC 575 ATOM 453 2HD BLYS 30 -6.606 28.094 21.037 0.50 24.54 1PLC 576 ATOM 454 1HE ALYS 30 -5.138 27.298 23.130 0.50 22.69 1PLC 577 ATOM 455 1HE BLYS 30 -4.709 26.867 22.883 0.50 25.84 1PLC 578 ATOM 456 2HE ALYS 30 -4.956 28.735 23.845 0.50 23.28 1PLC 579 ATOM 457 2HE BLYS 30 -6.257 27.063 23.262 0.50 25.75 1PLC 580 ATOM 458 1HZ ALYS 30 -7.360 28.765 23.779 0.50 21.25 1PLC 581 ATOM 459 1HZ BLYS 30 -6.721 25.740 21.353 0.50 26.03 1PLC 582 ATOM 460 2HZ ALYS 30 -7.206 27.240 23.677 0.50 21.83 1PLC 583 ATOM 461 2HZ BLYS 30 -5.279 25.211 21.533 0.50 25.17 1PLC 584 ATOM 462 3HZ ALYS 30 -6.682 27.986 24.852 0.50 21.60 1PLC 585 ATOM 463 3HZ BLYS 30 -6.289 25.095 22.599 0.50 25.92 1PLC 586 |
By default Leap will use the A conformation and disregard the others. This is fine for our purposes here. If we specifically wanted to start out in one of the other confirmations we would need to remove the A conformation from the file.
The final thing we need to do is add a TER card between our copper atom and our first crystallographic water atom. We will be adding the bonds to the copper atom manually within Leap since it is not strictly part of the protein chain. Hence the TER cards either side of it act to stop Leap trying to make it part of the protein chain and getting upset.
Here is the pdb file after the modifications above: 1PLC_mod_final.pdb
(Note: These tutorials are meant to provide
illustrative examples of how to use the AMBER software suite to carry out
simulations that can be run on a simple workstation in a reasonable period of
time. They do not necessarily provide the optimal choice of parameters or
methods for the particular application area.)
Copyright Ross Walker 2008