[gmx-users] isopeptide bond
Mark Abraham
Mark.Abraham at anu.edu.au
Sun Mar 13 23:32:11 CET 2011
On 13/03/2011 10:05 PM, Yulian Gavrilov wrote:
> Yes, I checked topol.top. There are all isopeptide bonds ,that I want
> (according to atom contacts, angles, etc.)
Perhaps I've been labouring under a misapprehension. You've mentioned an
isopeptide bond, which usually happens between a side-chain carboxylic
acid (GLU,ASP) and a side-chain amino acid (LYS), but also you've
mentioned GLY, which only has a backbone carbonyl. My brain read "GLY"
as "GLU". I would not expect pdb2gmx to cope correctly with terminating
the glycine via specbond.dat. Please show us the [atoms] and [bonds]
section for LYQ and GLYQ in your .top file.
There were other points I made in an early email to which you've not
responded, also.
Mark
>
> 2011/3/13 Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto: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
>> <mailto: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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