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

[SHAHEE ISLAM]

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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>