Right. Even if you somehow force pdb2gmx to write a topology in this case, the
bonds are not correct and the termini are incomplete. That will hopefully be
resolved when the bug is fixed. For now, you have a workaround. Just use
"-chainsep interactive" and you will get a proper topology.
-Jus
Hsin-Lin Chiang wrote:
I suspect this is a bug, so I have filed an issue on redmine:
http://redmine.gromacs.org/issues/784
In a previous issue (http://redmine.gromacs.org/issues/544), the "-chainsep
interactive" option did not work, but now it does. Conversely, "-chainsep ter"
(which shoul
>I suspect this is a bug, so I have filed an issue on redmine:
>
>http://redmine.gromacs.org/issues/784
>
>In a previous issue (http://redmine.gromacs.org/issues/544), the "-chainsep
>interactive" option did not work, but now it does. Conversely, "-chainsep ter"
>(which should also work in this c
I suspect this is a bug, so I have filed an issue on redmine:
http://redmine.gromacs.org/issues/784
In a previous issue (http://redmine.gromacs.org/issues/544), the "-chainsep
interactive" option did not work, but now it does. Conversely, "-chainsep ter"
(which should also work in this case)
Hsin-Lin Chiang wrote:
**> Please post a diff of the two topologies (the one that failed and
the one that
> worked).
>
> -Justin
I use diff bash commend on the two top file and save to log file.
The different was long but they both have three inter-disulfide bond
There are 3973 lines in dif
> Please post a diff of the two topologies (the one that failed and the one
> that
> worked).
>
> -Justin
I use diff bash commend on the two top file and save to log file.
The different was long but they both have three inter-disulfide bond
There are 3973 lines in different log file.
I'm not
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
>
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
Hsin-Lin Chiang wrote:
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 nee
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
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