[gmx-users] maximum number of specbonds?
Soren Wacker
swacker at ucalgary.ca
Thu Jun 19 19:01:37 CEST 2014
Something is really weird about that system.
The error message changes with the number of residues I use.
Everything works fine for 2 and 3 residues. With 4 residues I get :
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Warning: Starting residue DUL1 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue DUL2 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue DUL3 in chain not identified as Protein/RNA/DNA.
Warning: Starting residue DUL4 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
11 out of 11 lines of specbond.dat converted successfully
Special Atom Distance matrix:
DUL1 DUL1 DUL1 DUL2 DUL2 DUL2 DUL3
DU01 DU12 DU23 DU04 DU15 DU26 DU07
DUL1 DU12 0.200
DUL1 DU23 0.346 0.200
DUL2 DU04 0.400 0.346 0.529
DUL2 DU15 0.529 0.400 0.529 0.200
DUL2 DU26 0.529 0.346 0.400 0.346 0.200
DUL3 DU07 0.400 0.600 0.721 0.693 0.872 0.916
DUL3 DU18 0.200 0.400 0.529 0.529 0.693 0.721 0.200
DUL3 DU29 0.200 0.346 0.400 0.600 0.721 0.693 0.346
DUL4 DU010 0.400 0.529 0.721 0.400 0.600 0.721 0.400
DUL4 DU111 0.346 0.400 0.600 0.200 0.400 0.529 0.529
DUL4 DU212 0.200 0.200 0.400 0.200 0.346 0.400 0.529
DUL3 DUL3 DUL4 DUL4
DU18 DU29 DU010 DU111
DUL3 DU29 0.200
DUL4 DU010 0.346 0.529
DUL4 DU111 0.400 0.529 0.200
DUL4 DU212 0.346 0.400 0.346 0.200
Linking DUL-1 DU0-1 and DUL-1 DU1-2...
Linking DUL-1 DU0-1 and DUL-3 DU1-8...
Linking DUL-1 DU0-1 and DUL-3 DU2-9...
Linking DUL-1 DU0-1 and DUL-4 DU2-12...
Linking DUL-1 DU1-2 and DUL-1 DU2-3...
Linking DUL-1 DU1-2 and DUL-4 DU2-12...
Linking DUL-2 DU0-4 and DUL-2 DU1-5...
Linking DUL-2 DU0-4 and DUL-4 DU1-11...
Linking DUL-2 DU0-4 and DUL-4 DU2-12...
Linking DUL-2 DU1-5 and DUL-2 DU2-6...
Linking DUL-3 DU0-7 and DUL-3 DU1-8...
Linking DUL-3 DU1-8 and DUL-3 DU2-9...
Linking DUL-4 DU0-10 and DUL-4 DU1-11...
Linking DUL-4 DU1-11 and DUL-4 DU2-12...
Segmentation fault (core dumped)
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and with 5 residues:
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inking DUL-1 DU0-1 and DUL-1 DU1-2...
Linking DUL-1 DU0-1 and DUL-3 DU1-8...
Linking DUL-1 DU0-1 and DUL-3 DU2-9...
Linking DUL-1 DU0-1 and DUL-4 DU2-12...
Linking DUL-1 DU1-2 and DUL-1 DU2-3...
Linking DUL-1 DU1-2 and DUL-4 DU2-12...
Linking DUL-2 DU0-4 and DUL-2 DU1-5...
Linking DUL-2 DU0-4 and DUL-4 DU1-11...
Linking DUL-2 DU0-4 and DUL-4 DU2-12...
Linking DUL-2 DU0-4 and DUL-5 DU2-15...
Linking DUL-2 DU1-5 and DUL-2 DU2-6...
Linking DUL-2 DU1-5 and DUL-5 DU2-15...
Linking DUL-3 DU0-7 and DUL-3 DU1-8...
Linking DUL-3 DU1-8 and DUL-3 DU2-9...
Linking DUL-4 DU0-10 and DUL-4 DU1-11...
Linking DUL-4 DU1-11 and DUL-4 DU2-12...
Linking DUL-5 DU0-13 and DUL-5 DU1-14...
Linking DUL-5 DU1-14 and DUL-5 DU2-15...
Opening force field file /home/swacker/System/gromacs/GMX46/amber99sb-ildn.ff/aminoacids.arn
Opening force field file /home/swacker/System/gromacs/GMX46/amber99sb-ildn.ff/dna.arn
Opening force field file /home/swacker/System/gromacs/GMX46/amber99sb-ildn.ff/rna.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 5 residues with 15 atoms
Making bonds...
-------------------------------------------------------
Program gmx pdb2gmx, VERSION 5.1-dev-20140607-3db1d85
Source code file: /home/swacker/Install_Software/gromacs/src/gromacs/gmxpreprocess/pgutil.c, line: 125
Fatal error:
Residue 1 named DUL of a molecule in the input file was mapped
to an entry in the topology database, but the atom used in
an interaction of type special bond in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be
fixed.
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my specbonds.dat:
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11
CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
CYS SG 1 HEM FE 2 0.25 CYS2 HEME
CYS SG 1 HEM CAB 1 0.18 CYS2 HEME
CYS SG 1 HEM CAC 1 0.18 CYS2 HEME
HIS NE2 1 HEM FE 1 0.2 HIS1 HEME
MET SD 1 HEM FE 1 0.24 MET HEME
CO C 1 HEME FE 1 0.19 CO HEME
CYM SG 1 CYM SG 1 0.2 CYS2 CYS2
DUL DU0 4 DUL DU1 4 0.2 DUL DUL
DUL DU0 4 DUL DU2 4 0.2 DUL DUL
DUL DU1 4 DUL DU2 4 0.2 DUL DUL
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example.pdb
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TITLE PMX MODEL
REMARK THIS IS A SIMULATION BOX
CRYST1 36.770 36.770 36.770 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 DU0 DUL L 1 16.653 16.052 18.385 1.00 0.00
ATOM 2 DU1 DUL L 1 14.921 17.052 18.385 1.00 0.00
ATOM 3 DU2 DUL L 1 13.189 16.052 18.385 1.00 0.00
ATOM 4 DU0 DUL L 2 16.653 20.052 18.385 1.00 0.00
ATOM 5 DU1 DUL L 2 14.921 21.052 18.385 1.00 0.00
ATOM 6 DU2 DUL L 2 13.189 20.052 18.385 1.00 0.00
ATOM 7 DU0 DUL L 3 20.117 14.052 18.385 1.00 0.00
ATOM 8 DU1 DUL L 3 18.385 15.052 18.385 1.00 0.00
ATOM 9 DU2 DUL L 3 16.653 14.052 18.385 1.00 0.00
ATOM 10 DU0 DUL L 4 20.117 18.052 18.385 1.00 0.00
ATOM 11 DU1 DUL L 4 18.385 19.052 18.385 1.00 0.00
ATOM 12 DU2 DUL L 4 16.653 18.052 18.385 1.00 0.00
ATOM 13 DU0 DUL L 5 20.117 22.052 18.385 1.00 0.00
ATOM 14 DU1 DUL L 5 18.385 23.052 18.385 1.00 0.00
ATOM 15 DU2 DUL L 5 16.653 22.052 18.385 1.00 0.00
ATOM 16 DU0 DUL L 6 23.581 16.052 18.385 1.00 0.00
ATOM 17 DU1 DUL L 6 21.849 17.052 18.385 1.00 0.00
ATOM 18 DU2 DUL L 6 20.117 16.052 18.385 1.00 0.00
ATOM 19 DU0 DUL L 7 23.581 20.052 18.385 1.00 0.00
ATOM 20 DU1 DUL L 7 21.849 21.052 18.385 1.00 0.00
ATOM 21 DU2 DUL L 7 20.117 20.052 18.385 1.00 0.00
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aminoacids.rtp entry:
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[ DUL ]
[ atoms ]
DU0 DUM 0.000 1
DU1 DUM 0.000 2
DU2 DUM 0.000 3
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