[gmx-users] About -chainsep and -ter
Justin A. Lemkul
jalemkul at vt.edu
Thu Jul 21 13:37:16 CEST 2011
Hsin-Lin Chiang wrote:
> 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
>>> > 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
>>> > 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
>>> > 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
>> 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
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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