[gmx-users] About -chainsep and -ter

2011-07-21 Thread Hsin-Lin Chiang
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

Re: [gmx-users] About -chainsep and -ter

2011-07-21 Thread Justin A. Lemkul
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

[gmx-users] About -chainsep and -ter

2011-07-21 Thread Hsin-Lin Chiang
>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

Re: [gmx-users] About -chainsep and -ter

2011-07-21 Thread Justin A. Lemkul
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)

Re: [gmx-users] About -chainsep and -ter

2011-07-21 Thread Justin A. Lemkul
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

[gmx-users] About -chainsep and -ter

2011-07-21 Thread Hsin-Lin Chiang
> 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

Re: [gmx-users] About -chainsep and -ter

2011-07-21 Thread Justin A. Lemkul
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 >

[gmx-users] About -chainsep and -ter

2011-07-20 Thread Hsin-Lin Chiang
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

Re: [gmx-users] About -chainsep and -ter

2011-07-20 Thread Justin A. Lemkul
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

[gmx-users] About -chainsep and -ter

2011-07-20 Thread Hsin-Lin Chiang
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