[gmx-users] LINCS warning in md run

Thu Sep 13 11:50:25 CEST 2012

Ah okey. Thank you.
I will write them.

Hmm, but the protein is a crystal structure from pdb with a resolution of
1.2. I already added the hydrogen atoms to this structure and there I
already minimized them and made a md run. And there were no errors. And
now I only added the phosphate to the minimized structure. So I thought
that I only had to minimize the phosphate and the residue it bound on.
Or is there a mistake in my thought here?
>
>
> On 9/13/12 4:22 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Hi Justin,
>>
>> this atom is the CG atom of the phosphate I added to the protein.
>> But how can I find out by what it is punished?
>>
>
> Visualization.
>
>> This is the topology for this residue in the aminoacid.rtp file. I added
>> it manually. The parameter are from the amber parameter database
>> (http://www.pharmacy.manchester.ac.uk/bryce/amber/):
>>
>> [ TYP ]
>>   [ atoms ]
>>       N    N           -0.516300    1
>>      CA    CT           0.275503    2
>>      HA    H1           0.008223    3
>>      CB    CT          -0.354052    4
>>     HB1    HC           0.110326    5
>>     HB2    HC           0.110326    6
>>      CG    CA           0.119728    7
>>     CD1    CA          -0.198938    8
>>     HD1    HA           0.137143    9
>>     CE1    CA          -0.284884   10
>>     HE1    HA           0.177179   11
>>      CZ    C            0.452616   12
>>      OH    OS          -0.534452   13
>>       H    H            0.293600   14
>>     CE2    CA          -0.284884   15
>>     HE2    HA           0.177179   16
>>     CD2    CA          -0.198938   17
>>     HD2    HA           0.137143   18
>>       C    C            0.536600   19
>>       O    O           -0.581900   20
>>       P    P            1.393213   21
>>     OP1    OH          -0.752821   22
>>     OP2    O2          -0.822464   23
>>     OP3    O2          -0.822464   24
>>     H1P    HO           0.423316   25
>>   [ bonds ]
>>       N     H
>>       N    CA
>>      CA    HA
>>      CA    CB
>>      CA     C
>>      CB   HB1
>>      CB   HB2
>>      CB    CG
>>      CG   CD1
>>      CG   CD2
>>     CD1   HD1
>>     CD1   CE1
>>     CE1   HE1
>>     CE1    CZ
>>      CZ    OS
>>      CZ   CE2
>>      OS     P
>>     CE2   HE2
>>     CE2   CD2
>>     CD2   HD2
>>       C     O
>>      -C     N
>>       P   OP1
>>       P   OP2
>>       P   OP3
>>     OP1   H1P
>>
>> [ impropers ]
>>      -C    CA     N     H
>>      CA    +N     C     O
>>      CG   CE2   CD2   HD2
>>      CZ   CD2   CE2   HE2
>>     CD1    CZ   CE1   HE1
>>      CG   CE1   CD1   HD1
>>     CD1   CD2    CG    CB
>>     CE1   CE2    CZ    OH
>>
>>
>> Additionally I had to add an entry in the ffbonded file in the part [
>> dihedraltypes ]
>>
>> CA  CA  C   OS       4      180.00     4.60240     2    ;
>>
>> Here I am not completely sure about the entry because I could not find a
>> source for this combination of atoms.
>> But there is already an entry for the combination
>> CA  CA  C OH
>> Which has the same parameters.
>> Could this be the problem?
>>
>> And if it could be, can you please give me hint where I can find
>> parameters for it? Because I really could not find it.
>>
>
> Potentially - if you haphazardly assign parameters, you may get unexpected
> results.  There is a cited reference for the TYP parameters at the website
> above.  I would suggest looking there first, and if there is nothing
> listed,
> then contact the corresponding author of the study that first used/derived
> the
> parameters.
>
> Additionally, if you freeze a part of the protein's structure, you prevent
> any
> existing clashes from being resolved.  That may be the root of the issue.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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