Fahimeh Baftizadeh wrote:
Hello
I have to question.
1- I am generating a gro and toplogy file from a pdb file, usign
pdb2gmx.
the pdb file contains 18 separate chains, in each chain, there are 6
residues.
When I generate the topology and coordinates, it creates 18
posres-protein$i.itp file and 18 topol-protein$i.itp file and then
one topol.top and one conf.gro ...
is it normal?
Yes, pdb2gmx will write topologies for whatever molecules it finds (and
obviously has .rtp entries for).
i think it is just the position restraint for separate chains ... in
this way i think it enables me to restraint them separately if i
want? right?
Yes.
2- using topol.top and conf.gro, after solvating the molecule in the
box of water ... with editconf and genbox ... I am trying to
generate a tpr file, but when it generate it writes the following:
Generated 2211 of the 2211 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2211 of the 2211 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 3 bonded neighbours molecule type 'Protein2'
Excluding 3 bonded neighbours molecule type 'Protein3'
Excluding 3 bonded neighbours molecule type 'Protein4'
Excluding 3 bonded neighbours molecule type 'Protein5'
Excluding 3 bonded neighbours molecule type 'Protein6'
Excluding 3 bonded neighbours molecule type 'Protein7'
Excluding 3 bonded neighbours molecule type 'Protein8'
Excluding 3 bonded neighbours molecule type 'Protein9'
Excluding 3 bonded neighbours molecule type 'Protein10'
Excluding 3 bonded neighbours molecule type 'Protein11'
Excluding 3 bonded neighbours molecule type 'Protein12'
Excluding 3 bonded neighbours molecule type 'Protein13'
Excluding 3 bonded neighbours molecule type 'Protein14'
Excluding 3 bonded neighbours molecule type 'Protein15'
Excluding 3 bonded neighbours molecule type 'Protein16'
Excluding 3 bonded neighbours molecule type 'Protein17'
Excluding 3 bonded neighbours molecule type 'Protein18'
Excluding 2 bonded neighbours molecule type 'SOL'
what is this telling me? I didn't find a solution searching in the
mailing list?!
This is completely normal output. Please see the manual, section 5.4 and the
footnotes of Table 5.4 for the specifics of the nrexcl value.
-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
========================================
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