[gmx-users] N-terminus problem

[Emine Deniz Tekin]

Hi Mark,

Thank you for your reply.

Let me explain the problem a little more and answer your questions. I would
be happy if you could expound upon your reply.

      Hi Gromacs users,

I created a lipopeptide (lauroic acid  connected to an 8-residue peptide
> which starts with Valine).
>
>     How is the link from acid to peptide created?
>
> The link between acid and peptide is a “peptide bond”.
>
> (I prepared the *rtp *entry for the lauroic acid make a peptide bond as if lauroic acid was an amino acid (following your suggestion)).
>
>
>  If I try to use “pdb2gmx” for ONE LİPOPEPTİDE (9 residues), that is
>
>          pdb2gmx –f one_lipopeptide.pdb -ter
>
> It seems to work. That is, topol.top is created. (And also this topology
> works  for MD.)
>
>
>  Does that topology work for MD? Why does pdb2gmx think there's 9
> residues, and below there seem to be 63?
>
·                  But, if I try to use “pdb2gmx” for SEVEN LİPOPEPTİDE at
desired positions (63 residues), that is

            pdb2gmx –f seven_lipopeptide.pdb -ter
      It gives the fatal error: “Atom N not found in residue seq.nr. 1 while
adding improper”

> While I was creating the lipopeptide, I introduced the lauroic acid as a
> pseudo amino acid (following Mark’s suggestion). So, I really do NOT have
> atom N in the first residue. I pasted a part of my gro file below.
>
>  Some improper in your topology database entries wants a N atom that
> doesn't exist. Unfortunately, we don't have anywhere near enough information
> to guess why. pdb2gmx is trying to match your .rtp and specbond entries to
> your .gro file, but only seeing the latter can't help diagnose a mismatch.
> Some description of "desired positions" is also important.
>

    I wrote  a code to put 7 identical lipopeptides at desired positions.
That is, 7 lipopeptides are placed on a plane with 15 degree angle between
the adjacent lipopeptides.


>
> Also, giving full command lines are always preferred. You may not think
> anything significant is there, and you might be right, but if there *can* be
> something significant there, and we aren't given the chance to know whether
> it is present, we might just not bother to waste time guessing :)
>

I used gromos53a6 force field (extended to include lauroic acid parameters)
& spc type water


>   And also, I have a question: The first residue in my pdb file is lauroic
acid that is DPP, second residue is Valine and so on.. But when I used the
pdb2gmx with –ter it says: Start terminus VAL-2: None, End terminus ASP-9:
COO-) Would not DPP residue be the start terminus?

Best regards,

Mark

> Deniz
>
>
>   GROMACS molecule input test
>
> 574
>
>     1DPP     CA    1  11.027   5.295   3.153
>
>     1DPP     CB    2  10.894   5.299   3.078
>
>     1DPP     CG    3  10.777   5.234   3.153
>
>     1DPP     CD    4  10.645   5.254   3.078
>
>     1DPP     CE    5  10.521   5.203   3.153
>
>     1DPP     CZ    6  10.392   5.251   3.086
>
>     1DPP     CM    7  10.266   5.207   3.161
>
>     1DPP     CN    8  10.140   5.272   3.103
>
>     1DPP     CO    9  10.014   5.221   3.172
>
>     1DPP     CP   10   9.885   5.279   3.112
>
>     1DPP     CQ   11   9.761   5.203   3.160
>
>     1DPP      C   12  11.101   5.430   3.147
>
>     1DPP      O   13  11.032   5.531   3.136
>
>     2VAL      N   14  11.235   5.450   3.160
>
>     2VAL      H   15  11.249   5.550   3.159
>
>     2VAL     CA   16  11.368   5.385   3.181
>
>     2VAL     CB   17  11.390   5.233   3.181
>
>     2VAL    CG1   18  11.332   5.172   3.308
>
>     2VAL    CG2   19  11.338   5.161   3.056
>
>     2VAL      C   20  11.486   5.449   3.103
>
>     2VAL      O   21  11.498   5.436   2.982
>
>     …………..
>
>    63ASP    OD1  570  -0.306  14.874   3.343
>
>    63ASP    OD2  571  -0.451  15.030   3.289
>
>    63ASP      C  572  -0.057  15.023   3.106
>
>    63ASP     O1  573   0.014  15.003   3.207
>
>    63ASP     O2  574  -0.029  15.104   3.017
>
>   16.23937   16.23937   16.23937
>
>
>   I am using Gromacs 53a6 force field and gromacs 4.5.3 version.
>
> Any help will be appreciated.
>
>  Thanks in advance
>
>
>
> Deniz
>
>
>
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