Anna Marabotti wrote:
Dear gmx-users,
first let me resume my attempts on this question.
1) Using:
pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top
I obtained a .gro file in which the numbering of each chain correctly
starts from 21 to 379 in both chains, but no chain ID is present, so I
cannot distinguish residues of chain A from residues of chain B
2) Using:
pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top -renum
I obtained a .gro file in which the numbering of each chain starts from 1
to 359 in both chains (i.e. the second chain does not continue the numbering
from 360), but no chain ID is present, so again I cannot distinguish
residues of chain A from residues of chain B
3) Using:
pdb2gmx -f my_protein.pdb -o my_protein.gro -p my_protein.top -chainsep id
I obtained a .gro file in which the numbering of each chain starts from 21
to 379 in both chains (i.e. the second chain does not continue the numbering
from 360), but no chain ID is present, so again I cannot distinguish
residues of chain A from residues of chain B.
4) Using:
pdb2gmx -f my_protein.pdb -o my_protein.pdb -p my_protein.top
I obtained an output .pdb file in which the numbering and the chain ID of
the input .pdb file are kept (and so I can distinguish between the residues
of chain A and of chain B. However, when I continue with editconf+genbox and
add 22586 water molecules, I have the problem of more than 9999 residues,
which is not compatible with a .pdb format, so the numbering of the residues
restarts twice from zero.
My question is: can I distinguish chain A and B of my protein (either with a
chain ID or with a consecutive numbering of the two chains) AND have a file
format compatible with more than 9999 residues using Gromacs only?
Probably not. The .gro format allows for a bit more flexibility in residue
numbering, but no chain identifiers; vice versa for .pdb.
Careful creation of index files will allow you to circumvent both problems.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
