[gmx-users] N-terminus problem

[Emine Deniz Tekin]

Hi Gromacs users,


I created a lipopeptide (lauroic acid  connected to an 8-residue peptide
which starts with Valine).

·         If I try to use pdb2gmx with -ter flag   (Start terminus VAL-2:
None, End terminus ASP-9: COO-), everything seems to work (topology is
created.).

·         But, if I try to use pdb2gmx with -ter flag  for more than one
lipopeptide at desired positions, it gives the following error. (again says
Start terminus VAL-2: None, End terminus ASP-9: COO- )

 *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.


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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