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

[SHAHEE ISLAM]

thank you so much for your reply.

On 5/28/18, Soham Sarkar <soham9038 at gmail.com> wrote:
>  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
>> >>> --
>> >>> Gromacs Users mailing list
>> >>>
>> >>> * Please search the archive at
>> >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >>> posting!
>> >>>
>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>>
>> >>> * For (un)subscribe requests visit
>> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> >>> send a mail to gmx-users-request at gromacs.org.
>> >>>
>> >> --
>> >> Gromacs Users mailing list
>> >>
>> >> * Please search the archive at
>> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> >> posting!
>> >>
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
>> >> * For (un)subscribe requests visit
>> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send
>> >> a
>> >> mail to gmx-users-request at gromacs.org.
>> >>
>> >
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
>
> --
> SOHAM SARKAR
> Junior Research Fellow
> Department of Chemistry
> INDIAN INSTITUTE OF TECHNOLOGY BOMBAY
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
> mail to gmx-users-request at gromacs.org.
>