[gmx-users] Adding TPO and SEP to amber99sb-ildn.ff - question to aminoacids.hdb entry and "[impropers]" entry in aminoacids.rtp

[Justin Lemkul]

On 10/4/17 1:59 PM, Robert König wrote:
> Hi,
> I try to add the two AA SEP and TPO to the AMBER99SB-ILDN FF in GROMACS 2016.3. following the instructions on
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
> I added TPO and SEP to aminoacids.rtp like:
> [ TPO ] ; Phosphothreonine from http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_thp.lib
> ; changed: PS=P, OPA=O1P, OPB=O2P, OPC=O3P
>   [ atoms ] ; !entry.THP.unit.atoms table
>       N    N           -0.493700    1
>       H    H            0.301800    2
>      CA    CT          -0.1740      3
>      HA    H1           0.016400    4
>      CB    CT           0.15310     5
>      HB    H1          -0.090900    6
>     CG2    CT          -0.16170     7
>    HG21    HC           0.049600    8
>    HG22    HC           0.049600    9
>    HG23    HC           0.049600   10
>     OG1    OS          -0.637500   11
>       P    P            1.400      12
>     O1P    O2          -0.850      13
>     O2P    O2          -0.850      14
>     O3P    O2          -0.850      15
>       C    C            0.673100   16
>       O    O           -0.585400   17
>   [ bonds ] ; !entry.THP.unit.connectivity table
>       N     H
>       N    CA
>      CA    HA
>      CA    CB
>      CA     C
>      CB    HB
>      CB   CG2
>      CB   OG1
>     CG2  HG21
>     CG2  HG22
>     CG2  HG23
>     OG1    PS
>       S   O1P
>       S   O2P
>       S   O3P
>       C     O
>      -C     N   ; is present everywhere else
>   [ impropers ] ; is present everywhere else
>      -C    CA     N     H
>      CA    +N     C     O
>
> [ SEP ] ; Phosphoserine from http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_sep.lib
> ; changed: PS=P, OPA=O1P, OPB=O2P, OPC=O3P
>   [ atoms ] ; !entry.SEP.unit.atoms table
>       N    N           -0.493700    1
>       H    H            0.301800    2
>      CA    CT          -0.238000    3
>      HA    H1           0.093700    4
>      CB    CT           0.078200    5
>     HB2    H1          -0.060200    6
>     HB3    H1          -0.060200    7
>      OG    OS          -0.559300    8
>       P    P            1.4         9
>     O1P    O2          -0.850      10
>     O2P    O2          -0.850      11
>     O3P    O2          -0.850      12
>       C    C            0.673100   13
>       O    O           -0.585400   14
>   [ bonds ] ; !entry.THP.unit.connectivity table
>       N     H
>       N    CA
>      CA    HA
>      CA    CB
>      CA     C
>      CB   HB2
>      CB   HB3
>      CB    OG
>      OG    PS
>       S   O1P
>       S   O2P
>       S   O3P
>       C     O
>      -C     N   ; is present everywhere else
>   [ impropers ] ; is present everywhere else
>      -C    CA     N     H
>      CA    +N     C     O
> My first question is, like I commented, on both entries the last four lines are not in the parameters I got from
> http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_thp.lib and
> http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/amber_sep.libbut are found on all the other entries.So do I need these lines, are they right that way and what does it mean?

The functional form uses improper dihedrals to maintain planarity of the 
peptide bond. This may or may not be explicitly in every force field's 
files, or may be in places you're not looking.

The "-C N" line indicates that there's a bond between the preceding (-) 
residue and this one. GROMACS uses +/- connectivity to indicate bonds 
between residues in a chain.

> Second is in aminoacid.hdb.The entries look like:
> "THR    5"
> 1    1    H    N    -C    CA
> 1    5    HA    CA    N    CB    C
> 1    5    HB    CB    CA    CG2    OG1
> 3    4    HG2    CG2    CB    CA
> 1    2    HG1    OG1    CB    CA
> So I added till now:
> TPO     4
> 1               H
> 1               HA
> 1               HB
> 3               HG2
> SEP     4
> 1               H
> 1               HA
> 1               HB2
> 1               HB3
> is this right that far, especially TPO with 4 lines and 3 HG2?If somebody added these AA already I would be

Looks fine (assuming you've got the rest of those lines complete and not 
just this skeleton).

-Justin

> grateful for the missing parameters or a reliable source, I am not sure that my own estimations will be totally right.
> Thanks a lot!
> If you are still in good mood I would be very glad if you would a quick glance at my whole proceding. It is my first time to add residues and it would be good to know if I missed something or made a mistake.
> I followed http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
> 1. I added the parameter like in my first question.2. See my second question.3. Nothing - I didn't introduce new atom types
> 4. Nothing - I didn't require new bonded types
> 5. I added:TPO      Protein
> SEP      Proteinto residuetypes.dat6. Nothing - There is new special connectivity to other residues.
> So is that everything I have to do and do you see any mistakes?
> Thank you very much!Sincerly, olaf

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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