[gmx-users] About -chainsep and -ter
jiangsl at phys.sinica.edu.tw
Thu Jul 21 08:19:36 CEST 2011
於 2011/7/21 上午 03:19, gmx-users-request at 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.
>> > They seems to the same in my two chain system.
> There is likely some difference (probably a single bond) that is causing the
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