[gmx-users] Using specbond.dat in pdb2gmx
Matthew Stancea
mstancea at ggc.edu
Thu Jun 19 21:00:24 CEST 2014
(Ignore the earlier message)
>>> Ah, because it's Amber. Amber force fields are special and have specific
nomenclature that signifies N- and C-termini, so they automatically get built.
Changing the residue names by removing the N and C prefixes should fix things.
>> Okay, which file do I remove the N and C prefixes from?
>Coordinate file, always manipulate the coordinate file.
>But the fact that you're asking this tells me that likely you never actually
added those prefixes, so pdb2gmx is being "smart" and adding them for you. In
that case, there's nothing you can do short of (1) modifying the pdb2gmx code,
(2) manually hacking the topology - ugly, but effective, or (3) using a
different force field that doesn't have terminus-specific naming (anything
that's not Amber).
After discussing it with my professor, he believes that I can attempt both (2) and (3) until one of them works. Currently, he and I are going through the process of designing a script to perform (2).
Additionally, he told me that the only forcefields other than amber99sb that I can try are charmm27 and opls-aa. However, when I attempted to use either of those forcefields (these times I was relieved to finally see the option to select "none" for the termini), I received this error message:
-------------------------------------------------------
Program pdb2gmx_mpi, VERSION 4.6.2
Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2top.c, line: 1109
Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Does this have to do with the fact that I did select "none" for both terminals both of the times?
Here is the full command line:
"pdb2gmx_mpi -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i posre.itp -inter -ter"
And because I do not want to leave any information out, here is the full text for each of these (the difference between the two forcefields being the selection of the respective forcefields):
__________________________________________________________________________________________________________
:-) pdb2gmx_mpi (-:
Option Filename Type Description
------------------------------------------------------------
-f 1NB1.pdb Input Structure file: gro g96 pdb tpr etc.
-o conf.gro Output Structure file: gro g96 pdb etc.
-p topol.top Output Topology file
-i posre.itp Output Include file for topology
-n clean.ndx Output, Opt. Index file
-q clean.pdb Output, Opt. Structure file: gro g96 pdb etc.
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-chainsep enum id_or_ter Condition in PDB files when a new chain should
be started (adding termini): id_or_ter,
id_and_ter, ter, id or interactive
-merge enum no Merge multiple chains into a single
[moleculetype]: no, all or interactive
-ff string select Force field, interactive by default. Use -h for
information.
-water enum tip3p Water model to use: select, none, spc, spce,
tip3p, tip4p or tip5p
-[no]inter bool yes Set the next 8 options to interactive
-[no]ss bool no Interactive SS bridge selection
-[no]ter bool yes Interactive termini selection, instead of charged
(default)
-[no]lys bool no Interactive lysine selection, instead of charged
-[no]arg bool no Interactive arginine selection, instead of charged
-[no]asp bool no Interactive aspartic acid selection, instead of
charged
-[no]glu bool no Interactive glutamic acid selection, instead of
charged
-[no]gln bool no Interactive glutamine selection, instead of
neutral
-[no]his bool no Interactive histidine selection, instead of
checking H-bonds
-angle real 135 Minimum hydrogen-donor-acceptor angle for a
H-bond (degrees)
-dist real 0.3 Maximum donor-acceptor distance for a H-bond (nm)
-[no]una bool no Select aromatic rings with united CH atoms on
phenylalanine, tryptophane and tyrosine
-[no]ignh bool no Ignore hydrogen atoms that are in the coordinate
file
-[no]missing bool no Continue when atoms are missing, dangerous
-[no]v bool no Be slightly more verbose in messages
-posrefc real 1000 Force constant for position restraints
-vsite enum none Convert atoms to virtual sites: none, hydrogens
or aromatics
-[no]heavyh bool no Make hydrogen atoms heavy
-[no]deuterate bool no Change the mass of hydrogens to 2 amu
-[no]chargegrp bool yes Use charge groups in the .rtp file
-[no]cmap bool yes Use cmap torsions (if enabled in the .rtp file)
-[no]renum bool no Renumber the residues consecutively in the output
-[no]rtpres bool no Use .rtp entry names as residue names
Select the Force Field:
>From '/opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top':
1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
8: CHARMM27 all-atom force field (with CMAP) - version 2.0
9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
16: [DEPRECATED] Encad all-atom force field, using full solvent charges
17: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
18: [DEPRECATED] Gromacs force field (see manual)
19: [DEPRECATED] Gromacs force field with hydrogens for NMR
8
Using the Charmm27 force field in directory charmm27.ff
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/aminoacids.r2b
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/rna.r2b
Reading 1NB1.pdb...
Read 'KALATA B1', 376 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 29 residues with 376 atoms
chain #res #atoms
1 'A' 29 376
All occupancies are one
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/atomtypes.atp
Atomtype 1
Reading residue database... (charmm27)
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/aminoacids.rtp
Residue 44
Sorting it all out...
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/dna.rtp
Residue 48
Sorting it all out...
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/lipids.rtp
Residue 60
Sorting it all out...
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/rna.rtp
Residue 64
Sorting it all out...
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/aminoacids.hdb
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/dna.hdb
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/lipids.hdb
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/rna.hdb
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/dna.n.tdb
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/rna.n.tdb
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/dna.c.tdb
Opening force field file /opt/deploy/gromacs_4_6_2_mpi/share/gromacs/top/charmm27.ff/rna.c.tdb
Processing chain 1 'A' (376 atoms, 29 residues)
Which ARGININE type do you want for residue 24
0. Not protonated (charge 0) (ARGN)
1. Protonated (charge +1) (ARG)
Type a number:1
Which GLUTAMIC ACID type do you want for residue 3
0. Not protonated (charge -1) (GLU)
1. Protonated (charge 0) (GLUP)
Type a number:0
Identified residue CYS1 as a starting terminus.
Identified residue VAL29 as a ending terminus.
3 out of 3 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS1 CYS1 CYS5 CYS5 VAL6 CYS10 CYS10
N1 SG6 N47 SG52 C59 N101 SG106
CYS1 SG6 0.302
CYS5 N47 0.988 0.900
CYS5 SG52 1.070 0.917 0.333
VAL6 C59 1.498 1.396 0.510 0.585
CYS10 N101 1.122 0.901 0.614 0.609 0.835
CYS10 SG106 0.879 0.655 0.490 0.422 0.857 0.322
CYS15 N160 0.784 0.488 1.066 0.984 1.477 0.774 0.620
CYS15 SG165 0.477 0.202 0.960 0.961 1.432 0.823 0.625
CYS17 N184 1.030 0.784 0.721 0.460 1.004 0.617 0.387
CYS17 SG189 1.224 1.039 0.514 0.204 0.625 0.621 0.487
VAL21 C245 0.756 0.685 0.408 0.388 0.847 0.812 0.531
CYS22 N259 0.657 0.574 0.404 0.432 0.887 0.742 0.458
CYS22 SG264 0.755 0.588 0.371 0.430 0.827 0.436 0.203
VAL29 C363 0.132 0.394 1.117 1.193 1.626 1.248 1.004
CYS15 CYS15 CYS17 CYS17 VAL21 CYS22 CYS22
N160 SG165 N184 SG189 C245 N259 SG264
CYS15 SG165 0.320
CYS17 N184 0.661 0.767
CYS17 SG189 1.017 1.056 0.412
VAL21 C245 0.933 0.802 0.602 0.569
CYS22 N259 0.836 0.686 0.594 0.612 0.133
CYS22 SG264 0.701 0.606 0.533 0.568 0.419 0.321
VAL29 C363 0.854 0.555 1.137 1.345 0.869 0.777 0.886
Link CYS-1 N-1 and VAL-29 C-363 (y/n) ?y
Link CYS-1 SG-6 and CYS-15 SG-165 (y/n) ?y
Link CYS-5 SG-52 and CYS-17 SG-189 (y/n) ?y
Link CYS-10 SG-106 and CYS-22 SG-264 (y/n) ?y
Link VAL-21 C-245 and CYS-22 N-259 (y/n) ?y
Select start terminus type for CYS-1
0: NH3+
1: NH2
2: None
2
Start terminus CYS-1: None
Select end terminus type for VAL-29
0: COO-
1: COOH
2: CT2
3: CT3
4: None
4
End terminus VAL-29: None
-------------------------------------------------------
Program pdb2gmx_mpi, VERSION 4.6.2
Source code file: /home/msaum/apps/gromacs-4.6.2/src/kernel/pdb2top.c, line: 1109
Fatal error:
There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
__________________________________________________________________________________________________________
Matthew
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