[gmx-users] warning:Long Bond

[Justin Lemkul]

On 12/21/17 12:09 PM, Saleheh Heidari wrote:
> 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?

Long bonds mean either missing residues or bad input geometry.

> I generated my pdb file with NanoEngineer-1 software by Loomis Laboratory
> of Physics at UIUC (http://bionano.physics.illinios.edu)

A custom-made structure is unlikely to have missing residues, so likely 
your problem is distorted geometry. Check the atom numbers printed by 
pdb2gmx to see what's going on. Incorrect PDB format can also trigger 
this problem (not all programs write rigorously correct PDB files).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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