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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