[gmx-users] isopeptide bond

Sun Mar 13 12:05:05 CET 2011

Yes, I checked topol.top.  There are all isopeptide bonds ,that I want
(according to atom contacts, angles, etc.)

2011/3/13 Mark Abraham <Mark.Abraham at anu.edu.au>

>  On 13/03/2011 9:53 PM, Yulian Gavrilov wrote:
>
>  Thank you!
>
>  I use the correct “O” in Gly according to .rtp and I checked it with vmd.
> There is really a new isopeptide bond. When there is no bond, after
> minimization and equilibration, Gly and Lys just close to each other but
> they are not connected (in vmd). In my case they are connected (in vmd,
> pymol).
>
>
> None of these visualization programs read the topology in your .top file.
> They just make guesses based on the geometry of the atoms in the coordinate
> file. Anything you see that it guessed is irrelevant. Read your pdb2gmx
> output, and go and look at the topology to see what atoms have made a bond.
>
> Mark
>
>
>  When I look on step...pdb, one these residues is exploded (it's atoms are
> far from each other outside of the water box).
>
>
> 2011/3/13 Mark Abraham <Mark.Abraham at anu.edu.au>
>
>>  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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>
>
>
> --
>
> Sincerely,
>
> Yulian Gavrilov
>
>
>
> --
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-- 

Sincerely,

Yulian Gavrilov
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