[gmx-users] isopeptide bond

[Mark Abraham]

On 13/03/2011 8:55 PM, Yulian Gavrilov wrote:
>
> 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.
>

IIRC, this creates a bond between the lysine side-chain amine N and 
glycine *backbone* carbonyl C. You must use the atom name for the 
side-chain carbonyl carbon (see .rtp entry for GLY). If you've done this 
wrong, then specbond will probably not have made a bond, because the 
backbone carbonyl C was too far away. You should check your pdb2gmx 
output carefully.

>   1.
>
>
>   2.
>
>       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.
>

Seems like a reasonable hypothesis - but do look at 2454 and 2456 as 
well. You have to get out your trajectory and a visualization package 
and see what is actually going wrong. The warnings can be symptomatic of 
a problem that started elsewhere.

You say you've added new interaction types, but I see no reason why you 
would need to. It's chemically so similar to a backbone peptide that you 
may as well keep things the same and model it the same way. Regardless, 
you should probably check that the specbond.dat mechanism has created 
interactions that make sense. Compare with a normal peptide bond.

Mark

> Please can you advice me how yo make this isopeptide bond good?
>
> Can I just remove this hydrogens?
>
>
> -- 
>
> Sincerely,
>
> Yulian Gavrilov
>
>

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