Short description
The program works interactively, and should be straightforwardly to use. However, for some of the stages in the output a short description is given below.
P D B 2 A D F - program
version 2005.01
Written by: Marcel Swart, 2005
This program uses AMBER parameter files
see: http://amber.scripps.edu
Do you want a logfile to be written (Y/n) ?
This option exists to create a logfile of what pdb2adf does. However, it should normally be used only for debugging purposes.
Ignoring atom on line: ATOM 974 OH LYS A 128 -10.073 42.775 15.690 1.00 38.79 5AZU1065
This is a warning that the atom on that particular line is ignored, should normally occur only few times (less than ten). Depends also on how well the PDB file follows the PDB format rules.
Data Processed:
Nat: 2519
Nmol: 196
NChains: 1
Information about what has been read on the PDB file: the total number of atoms (Nat), number of molecules/residues (Nmol) and number of protein chains (Nchains).
Please wait, making connection tables
At this point, the connections between the atoms are being made by looking at atom distances. It may take a while, depending on the size of the system.
Do you want to make separate files for each chain (Y/n) ?
You have the option to make different inputfiles for different protein chains, but you can also make one inputfile for all of them together.
Found the following terminal amino acid residues : (C-term) 128 (N-term) 1 Do you want to use these as terminal residues (Y/n) ?
Info is given about the C- and N-terminal residue of each chain. Reported for making sure they are chosen correctly. Note, if the C- and N-terminal residues are connected (rarely the case probably), enter N here.
Multiple AMBER options for HIS : 0 Decide every time differently 1 HID Histidine Delta Hydrogen 2 HIE Histidine Epsilon Hydrogen 3 HIP Histidine E & D Hydrogens Suggested option: 0
For a number of residues (His, Glu, Asp, Lys and Cys) there is more than one option available in the AMBER95 force field, depending on the protonation state (His, Glu, Asp and Lys) or the existence of a sulphur bridge/connection to a metal atom (Cys). The default is to choose a different option for the His and Cys residues, and use one option for Glu, Asp and Lys (fully charged). However, if wanted you can make a choice for all residues.
Multiple AMBER options for CYS 3 ( 3) :
1 CYS Cysteine (SH)
2 CYM Deprotonated Cysteine (S-)
3 CYX Cystine (S-S bridge)
Connections and Nearest Atoms for SG CYS 3 SG ( P2A # 41 PDB# 20 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.82 38 19 CB CYS 3 CB 1 3.79 2382 980 O HOH 151 O
2 2.02 461 193 SG CYS 26 SG 2 3.80 22 0 HC GLN 2
3 4.04 2391 983 O HOH 154 O
4 4.15 509 206 O GLN 28 O
5 4.18 522 0 HA PHE 29
Suggestion: 3
The options for Cys3 are given, with information about the atoms bonded to the SG sulphur atom (on the left), as well as the closest five non-bonded atoms (on the right). This information may help you decide which choice to make for this particular residue. Also given (on the bottom) is the suggested choice, which is based, in this case, on the presence of a sulphur bridge.
Multiple AMBER options for HIS 46 ( 46) :
1 HID Histidine Delta Hydrogen
2 HIE Histidine Epsilon Hydrogen
3 HIP Histidine E & D Hydrogens
Connections and Nearest Atoms for ND HIS 46 ND1 ( P2A # 844 PDB# 347 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.37 843 346 CG HIS 46 CG 1 2.62 2166 0 H1 MET 121
2 1.33 846 349 CE HIS 46 CE1 2 3.23 2080 863 ND HIS 117 ND1
3 2.04 2318 959 CU CU 130 CU 3 HB 3.33 2163 900 S MET 121 SD
4 3.40 2164 901 CT MET 121 CE
5 3.57 2082 865 CE HIS 117 CE1
Connections and Nearest Atoms for NE HIS 46 NE2 ( P2A # 848 PDB# 350 )
Dist P2A Nr PDB Nr Label Near Dist P2A Nr PDB Nr Label
1 1.32 846 349 CE HIS 46 CE1 1 HB 2.70 162 67 O ASN 10 O
2 1.37 850 348 CD HIS 46 CD2 2 2.83 814 0 H1 MET 44
3 3.23 2166 0 H1 MET 121
4 3.52 822 332 O MET 44 O
5 3.74 813 334 CT MET 44 CG
Suggestion: 2
For His residues, the information is given for both the delta- and the epsilon nitrogen atoms. Also indicated (by HB) is the presence of a hydrogen bond with another atom. The definition used here is that two atoms are hydrogen bonded if they are both non-carbon/non-hydrogen atoms, and the distance between them is less than the sum of the van der Waals radii of the atoms. It is a simple definition, but seems to be effective. In this case, as the N(delta) is bonded to copper, the proton should be attached to the N(epsilon).
Making choice for which molecules should be QM, which MM
Now we come to the part where the division in the QM and MM systems is made.
Residues belonging to chain 0
Option Molecule Option Molecule Option Molecule Option Molecule Option Molecule
1: ALA 1 28: GLN 28 55: ASP 55 82: ALA 82 109: ALA 109
2: GLN 2 29: PHE 29 56: LYS 56 83: HIS 83 110: TYR 110
etc
All molecules/residues belonging to chain 0 are given, with an option number.
Give option number of molecules to be put in QM region (or 'c' to continue): Note: by specifying a negative number a molecule is removed from the QM region
Here you are asked to enter the option numbers of the residues you want to put in the QM system.
Putting GLY 45 in QM region Putting HIS 46 in QM region
In this case, Gly45 and His46 have been put in the QM system.
Make a choice for the QM/MM treatment of GLY 45
0: Put completely in QM region
1: Cut off at C-alpha (put NH in QM region, CO in MM region)
2: Cut off at C-alpha (put NH in MM region, CO in QM region)
3: Cut off at C-alpha (put NH and CO in MM region)
4: Cut off at C-alpha (put NH and CO in QM region, sidechain in MM region)
5: Put only part of sidechain in QM region
Suggestion: 2
Give choice:
A choice should be made for where to cut-off the QM system. Normally this is done at the C(alpha) position, and you should simply choose the Suggestion.
Solvent molecules (SOL/HOH) belonging to this chain:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
61 62 63 64 65 66
Give the number of the molecule to be put in QM region (or 'c' to continue):
Also water molecules can be put in the QM system.
Box Shape options: 1 Spherical box 2 Cubic box Make a choice:
Type of box to be used.
Maximum atomic distance (Angs) from center 25.62 Give boxsize (def.: 28.62 Angs)
Size of box to be used to put a layer of solvent molecules around the system. Max. dist. is the maximal distance of any protein atom from the center of mass of the protein. Usually you should choose a boxsize at least 6 Angstrom larger (so at least two solvent molecules are surrounding the system).
Using BOXSIZE value of 30.0000 Adding atoms for box 1 Added (Box): 0 (Total): 0 Excl. (1): 648 Excl. (2): 0 Adding atoms for box 2 Added (Box): 9 (Total): 9 Excl. (1): 639 Excl. (2): 0 ... Adding atoms for box 63 Added (Box): 3 (Total): 7635 Excl. (1): 645 Excl. (2): 0 Adding atoms for box 64 Added (Box): 0 (Total): 7635 Excl. (1): 648 Excl. (2): 0 Writing inputfile for chain 1A total amount of 7635 atoms (2545 water molecules) has been added.
Inputfile(s) written, everything processed, work has been done. Thank you for using the PDB2ADF program. ================================ Normal ending of PDB2ADF program ================================
ADF inputfile(s) have been written, the PDB-file has been processes. Everything is done.
