[gmx-users] gmx error

[Mark Abraham]

Hi,

I can't tell what you think the error is

Mark

On Fri, 15 Sep 2017 13:46 Rana Rehan Khalid <rrkhalid at umich.edu> wrote:

> Hi everybody
>
> I am facing this error kindly guide me
>
> hecking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 324 residues with 5193 atoms
> Chain time...
> Making bonds...
> Number of bonds was 5261, now 5260
> Generating angles, dihedrals and pairs...
> Before cleaning: 13851 pairs
> Before cleaning: 14001 dihedrals
> Keeping all generated dihedrals
> Making cmap torsions...
> There are 14001 dihedrals, 1053 impropers, 9524 angles
>           13737 pairs,     5260 bonds and     0 virtual sites
> Total mass 36926.509 a.m.u.
> Total charge -1.000 e
> Writing topology
> Processing chain 2 'B' (316 atoms, 39 residues)
> Analysing hydrogen-bonding network for automated assignment of histidine
>  protonation. 71 donors and 55 acceptors were found.
> There are 79 hydrogen bonds
> Will use HISE for residue 7
> Will use HISE for residue 29
> Identified residue LEU1 as a starting terminus.
> Identified residue THR39 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
>                     HIS7
>                    NE252
>    HIS29  NE2226   1.978
> Opening force field file /usr/share/gromacs/top/amber99sb.ff/aminoacids.arn
> Opening force field file /usr/share/gromacs/top/amber99sb.ff/dna.arn
> Opening force field file /usr/share/gromacs/top/amber99sb.ff/rna.arn
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 39 residues with 633 atoms
> Chain time...
> Making bonds...
> Number of bonds was 643, now 642
> Generating angles, dihedrals and pairs...
> Before cleaning: 1677 pairs
> Before cleaning: 1707 dihedrals
> Keeping all generated dihedrals
> Making cmap torsions...
> There are 1707 dihedrals,  137 impropers, 1154 angles
>           1665 pairs,      642 bonds and     0 virtual sites
> Total mass 4473.138 a.m.u.
> Total charge 4.000 e
> Writing topology
> Including chain 1 in system: 5193 atoms 324 residues
> Including chain 2 in system: 633 atoms 39 residues
> Now there are 5826 atoms and 363 residues
> Total mass in system 41399.647 a.m.u.
> Total charge in system 3.000
>
> regards
> --
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