Hsin-Lin Chiang wrote:
於 2011/7/21 上午 03:19, gmx-users-requ...@gromacs.org 提到:
Hi everyone,
> > My pdb file is consist of two chains with one intra- two
> inter-disulfide bonds.
> So I used pdb2gmx in this way
> pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q
-chainsep ter
> (I have deleted the TER and OXT lines of A-chain.)
> I'm not sure if I need to use -ter here, I don't understand the
meaning
> of "interective termini selection, iso charged ."
The -ter option allows you to change the protonation state of the
termini. The
shorthand "iso" means "instead of," implying that charged termini are the
default. If you do not need to alter the protonation state of the
termini, then
you do not need the -ter option.
Thanks for the explain.
> Anyway, I met problem after editconf, genbox, grompp, genion, and
grompp.
> When I execute mdrun,
> I got the warning and terminated.
> Please see the long message below my name.
Your system exploded because pdb2gmx likely tried to make your two
chains one
continuous protein, forming an unrealistic bond between the C-terminal
of chain
A and the N-terminal of chain B. By removing the TER delimiter, you've
essentially told pdb2gmx that you have one protein, not two.
If I don't use -chainsep ter, then pdb2gmx will consider two chains as
Protein-A and Protein-B.
The inter-disulfide bonds between two-chains will be lost.
> However, if I used pdb2gmx in this way
> pdb2gmx -f protein.pdb -o protein.gro -p protein.top -n -q -chainsep
> interactive
> and selected y.
> Then everything is OK in mdrun step.
> I don't know what the different in -chainsep interactive and
-chainsep
> ter is in my case.
Assuming that the "y" response indicates that you want separate
chains, that's
why this approach works. Regardless, if you have two distinct
proteins (i.e.
the backbones are not continuous), you do not want the chains to be
considered
continuous. Disulfides are created in a separate mechanism utilizing
specbond.dat and is independent of the use of -chainsep.
The question is ,
Merge chain ending with residue ASN21 (chain id 'A', atom 163OXT) with
chain starting with
residue PHE1 (chain id 'B', atom 165 N)? [n/y]
Then I choose y, I think it's the same as -chainsep ter. Isn' it?
But for -chainsep ter, there is errors in mdrun.
For -chainsep interactive and type "y", everything correct.
Please post a diff of the two topologies (the one that failed and the one that
worked).
-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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