Amit Choubey wrote:
hi everyone,
I am trying to set up a very small simulation with DPPC lipid. I am using
the GROMOS96 53a6 FF. Now i have my pdb file which looks like
ATOM 1 C33 DPPC 1 15.771 52.651 9.201 1.00 0.00
ATOM 2 C34 DPPC 1 16.750 52.953 11.353 1.00 0.00
ATOM 3 C35 DPPC 1 16.477 54.817 9.854 1.00 0.00
ATOM 4 N DPPC 1 16.796 53.384 9.947 1.00 0.00
ATOM 5 C32 DPPC 1 18.082 53.008 9.318 1.00 0.00
ATOM 6 C31 DPPC 1 19.292 53.957 9.530 1.00 0.00
ATOM 7 O32 DPPC 1 19.653 54.093 10.906 1.00 0.00
ATOM 8 P DPPC 1 20.931 54.971 11.160 1.00 0.00
ATOM 9 O33 DPPC 1 21.965 54.328 10.317 1.00 0.00
ATOM 10 O34 DPPC 1 20.513 56.372 10.957 1.00 0.00
ATOM 11 O31 DPPC 1 21.096 54.572 12.688 1.00 0.00
ATOM 12 C3 DPPC 1 20.436 55.317 13.711 1.00 0.00
ATOM 13 C2 DPPC 1 20.715 54.687 15.095 1.00 0.00
ATOM 14 O21 DPPC 1 20.250 55.525 16.189 1.00 0.00
ATOM 15 C21 DPPC 1 18.977 55.438 16.644 1.00 0.00
ATOM 16 O22 DPPC 1 18.253 54.474 16.407 1.00 0.00
ATOM 17 C22 DPPC 1 18.585 56.603 17.549 1.00 0.00
ATOM 18 C23 DPPC 1 17.728 56.214 18.751 1.00 0.00
ATOM 19 C24 DPPC 1 17.396 57.481 19.541 1.00 0.00
ATOM 20 C25 DPPC 1 16.456 57.200 20.713 1.00 0.00
ATOM 21 C26 DPPC 1 16.196 58.488 21.496 1.00 0.00
ATOM 22 C27 DPPC 1 15.247 58.258 22.678 1.00 0.00
ATOM 23 C28 DPPC 1 15.849 57.273 23.685 1.00 0.00
ATOM 24 C29 DPPC 1 14.863 56.871 24.797 1.00 0.00
ATOM 25 C210 DPPC 1 15.354 55.818 25.560 1.00 0.00
ATOM 26 C211 DPPC 1 14.405 55.341 26.675 1.00 0.00
Now for atoms C210, C211 etc (with three no. after the element name) the
pdb2gmx prints out following kind of warning
WARNING: atom C210 is missing in residue DPP 1 in the pdb file
Probably you've got the column-based formatting of the .pdb file wrong,
since "DPPC" is being truncated to "DPP". Try shifting that entry one
column left, keeping the rest in the same place.
Mark
WARNING: atom C211 is missing in residue DPP 1 in the pdb file
I am sure that it has to do with the way i am writing the pdb file (ie
format) . I am sure that the pdb2gmx is actually detecting the right kind of
molecule (DPPC) . But i cannot figure out how exactly to write my pdb file.
Thank you in advance
Amit
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
