[gmx-users] calculation of distance between the center of geometry of two proteins

[Soham Sarkar]

 use the latest .tpr formed after production run else try

tpbconv -s dynamic.tpr -o dynamic_new.tpr

On Mon, May 28, 2018 at 3:29 PM, SHAHEE ISLAM <islamshahee at gmail.com> wrote:

> thank you so much.
> after deleting from -select its now working.but the fatal error is
> Molecule in topology has atom numbers below and above natoms (565).
> You are probably trying to use a trajectory which does not match the
> first 565 atoms of the run input file.
> You can make a matching run input file with tpbconv.
>
>
> On 5/28/18, SHAHEE ISLAM <islamshahee at gmail.com> wrote:
> > after deleting -select
> > this error is coming
> > Invalid command line argument:
> > cog of group "Chain_A" plus cog of group "Chain_B"
> >
> >
> > On 5/28/18, Soham Sarkar <soham9038 at gmail.com> wrote:
> >> Delete from -select.. previous are ok
> >>
> >> On Mon, 28 May 2018, 3:12 pm SHAHEE ISLAM, <islamshahee at gmail.com>
> wrote:
> >>
> >>> hi,
> >>> to calculate the distance between the center of geometry of two
> >>> proteins, i am using this command
> >>> g_dist -f md_0_1_noPBC.xtc -s dynamic.tpr -n index.ndx -o distave.xvg
> >>> -select 'cog of group "Chain_A" plus cog of group "Chain_B"'
> >>> Invalid command line argument:
> >>> -select
> >>> here in this index file the two chain group name Chain_A and Chain_B
> >>> how i will select the two chain.
> >>>
> >>> thanking you
> >>> shahee islam
> >>> university of calcutta
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-- 
SOHAM SARKAR
Junior Research Fellow
Department of Chemistry
INDIAN INSTITUTE OF TECHNOLOGY BOMBAY