[gmx-users] isopeptide bond

[Yulian Gavrilov]

Dear gmx users,

I just started with gromacs.

Can you help me to find my mistake? I already asked about it, but I did not
understand what to do exactly in my case.

I try to run to add a new *isopeptide bone* to connect Lys and Gly (to make
a tetramer of *ubiquitin*). I use AMBER99 force field, Gromacs 4.0.5.

What I did:

   1.

   I changed names of residues according to AMBER rules (LYS to LYN etc.).
   2.

   Added new type of residues to ffamber.rtp (LYN -> LYQ and GLY -> GLQ that
   are making a new isopeptide bond) and added a new line to specbond.dat (LYN
   NZ 1 GLY C 1 0.13 LYQ GLQ) to make such a bond.
   3.

   Added new bond type, angle type and dihedral type to ffamber99bon.itp


 After running of MD (I've got good minimization and equilibration – nvt and
npt) I've got such an error:


 starting mdrun 'Protein in water'

600000 steps, 1200.0 ps.

step 94100, will finish Sun Mar 13 08:15:56 2011

Step 94124, time 188.248 (ps) LINCS WARNING

relative constraint deviation after LINCS:

rms 0.000796, max 0.032792 (between atoms 2454 and 2456)

bonds that rotated more than 30 degrees:

atom 1 atom 2 angle previous, current, constraint length

2454 2457 35.6 0.1522 0.1545 0.1522


 And after it the same type of errors with another atoms:

2454 2456 36.1 0.1106 0.1113 0.1090 --> *Gly CA and HA1, HA2*

2454 2455 40.5 0.1114 0.1103 0.1090

.....

 2454 2456 90.0 0.1078 0.1479 0.1090

771 773 48.5 0.1011 0.1012 0.1010

......

771 773 39.8 0.1012 0.1005 0.1010 --> *Gly NZ and HZ1, HZ2*

771 772 34.9 0.1012 0.1030 0.1010

.......

2454 2457 102.1 0.1490 38312886396780544.0000 0.1522

2454 2456 83.0 5.9313 39290317874135040.0000 0.1090

.......

First errors are with atoms from the residues with *new isopeptide bond*. I
suppose, that this bond is not good.

Please can you advice me how yo make this isopeptide bond good?

Can I just remove this hydrogens?

-- 

Sincerely,

Yulian Gavrilov
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110313/dce751af/attachment.html>