[gmx-users] warning:Long Bond

[Saleheh Heidari]

Dear Gromacs Users

I am trying to run a molecular dynamics simulation with a DNA tetrahedron.
I am using Gromacs-2016.4 having the forcefield AMBER99SB-ILDN.

The topology file has been successfully generated.

However I am concerned with the following comment in the output of pdb2gmx,
these are the gromacs output for the first chain:

################
There are 4 chains and 0 blocks of water and 220 residues with 4497 atoms

  chain  #res #atoms
  1 'A'    55   1119
  2 'B'    55   1133
  3 'C'    55   1123
  4 'D'    55   1122

All occupancies are one
Opening force field file
/usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/atomtypes.atp
Atomtype 67
Reading residue database... (amber99sb-ildn)
Opening force field file
/usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file
/usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.rtp
Residue 109
Sorting it all out...
Opening force field file
/usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.rtp
Residue 125
Sorting it all out...
Opening force field file
/usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb
Opening force field file
/usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.hdb
Opening force field file
/usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.hdb
Opening force field file
/usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb
Opening force field file
/usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.c.tdb
Processing chain 1 'A' (1119 atoms, 55 residues)
Identified residue DT51 as a starting terminus.
Identified residue DT355 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file
/usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn
Opening force field file
/usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/dna.arn
Opening force field file
/usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/rna.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 55 residues with 1747 atoms
Chain time...
Making bonds...
Warning: Long Bond (30-31 = 0.277244 nm)
Warning: Long Bond (62-63 = 0.306978 nm)
Warning: Long Bond (92-93 = 0.350789 nm)
Warning: Long Bond (124-125 = 0.320527 nm)
Warning: Long Bond (157-158 = 0.340453 nm)
Warning: Long Bond (189-190 = 0.273576 nm)
Warning: Long Bond (219-220 = 0.268338 nm)
Warning: Long Bond (251-252 = 0.277104 nm)
Warning: Long Bond (283-284 = 0.360828 nm)
Warning: Long Bond (315-316 = 0.320431 nm)
Warning: Long Bond (348-349 = 0.329925 nm)
Warning: Long Bond (381-382 = 0.334705 nm)
Warning: Long Bond (413-414 = 0.330311 nm)
Warning: Long Bond (477-478 = 0.354473 nm)
Warning: Long Bond (510-511 = 0.254489 nm)
Warning: Long Bond (542-543 = 0.659257 nm)
Warning: Long Bond (574-575 = 0.331438 nm)
Warning: Long Bond (606-607 = 0.757552 nm)
Warning: Long Bond (638-639 = 0.277172 nm)
Warning: Long Bond (670-671 = 0.307023 nm)
Warning: Long Bond (700-701 = 0.296372 nm)
Warning: Long Bond (730-731 = 0.296309 nm)
Warning: Long Bond (760-761 = 0.350757 nm)
Warning: Long Bond (792-793 = 0.273076 nm)
Warning: Long Bond (822-823 = 0.344508 nm)
Warning: Long Bond (855-856 = 0.25441 nm)
Warning: Long Bond (887-888 = 0.360906 nm)
Warning: Long Bond (919-920 = 0.320435 nm)
Warning: Long Bond (952-953 = 0.254546 nm)
Warning: Long Bond (984-985 = 0.35455 nm)
Warning: Long Bond (1017-1018 = 0.254603 nm)
Warning: Long Bond (1049-1050 = 0.307071 nm)
Warning: Long Bond (1079-1080 = 0.344648 nm)
Warning: Long Bond (1112-1113 = 0.254605 nm)
Warning: Long Bond (1144-1145 = 0.611147 nm)
Warning: Long Bond (1208-1209 = 0.514416 nm)
Warning: Long Bond (1241-1242 = 0.254576 nm)
Warning: Long Bond (1273-1274 = 0.360751 nm)
Warning: Long Bond (1337-1338 = 0.277311 nm)
Warning: Long Bond (1369-1370 = 0.354457 nm)
Warning: Long Bond (1402-1403 = 0.329893 nm)
Warning: Long Bond (1435-1436 = 0.334784 nm)
Warning: Long Bond (1467-1468 = 0.273162 nm)
Warning: Long Bond (1497-1498 = 0.29643 nm)
Warning: Long Bond (1527-1528 = 0.296213 nm)
Warning: Long Bond (1557-1558 = 0.268429 nm)
Warning: Long Bond (1589-1590 = 0.307397 nm)
Warning: Long Bond (1619-1620 = 0.344558 nm)
Warning: Long Bond (1652-1653 = 0.281585 nm)
Warning: Long Bond (1682-1683 = 0.350724 nm)
Number of bonds was 1878, now 1878
Generating angles, dihedrals and pairs...
Before cleaning: 4579 pairs
Before cleaning: 4964 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are 4964 dihedrals,  320 impropers, 3423 angles
          4414 pairs,     1878 bonds and     0 virtual sites
Total mass 16824.664 a.m.u.
Total charge -54.000 e
Writing topology
#####################

I would like to know the reason behind the Long Bond warnings, should I be
concerned and Is there any way to fix these?
I generated my pdb file with NanoEngineer-1 software by Loomis Laboratory
of Physics at UIUC (http://bionano.physics.illinios.edu)

Best ,

Saleheh Heydari