[gmx-users] warning:Long Bond

Wed Jan 3 22:26:18 CET 2018

Hi Justin

Thanks for your reply. As you said I checked the atom numbers which gave
the long bond warning, and there was no problem with the intra-residual
bonds in all the residues, but the warning was given for the inter-residual
bonds, i.e. the bond between the last atom of a residue and the first atom
of the next residue. I also checked the pdb file by visualizing it with VMD
and it looked correct. Should I continue and ignore the warnings assuming
that the structure returns to the proper conformation after minimization?

I would greatly appreciate your help.

Regards,

Saleheh Heydari

On Fri, Dec 22, 2017 at 3:22 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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/a
>> minoacids.n.tdb
>> Opening force field file
>> /usr/local/bin/gromacs/share/gromacs/top/amber99sb-ildn.ff/a
>> minoacids.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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>