On 4/3/18 5:50 AM, Joe Jordan wrote:
Gromacs 4.6 is no longer supported, so I would recommend upgrading to 2018
and using gmx select. Short of that, if you just run make_ndx and don't use
a selection sting you will get a group corresponding to NAP with the right
number of atoms.
Neither gmx select nor gmx make_ndx should be necessary here. All
defined [moleculetypes] are default index groups. The ligand should show
up as a choice from any GROMACS program without needing an index file at
all.
-Justin
On Tue, Apr 3, 2018 at 11:41 AM, abhisek Mondal <abhisek.m...@gmail.com>
wrote:
I'm using v4.6.2
$make_ndx -f npt.gro
r 306 (residue num of ligand)
name 24 Ligand
This should do the work right ?
On Tue, Apr 3, 2018 at 3:07 PM, Joe Jordan <e.jjorda...@gmail.com> wrote:
I got a group with the right number of atoms when I tried it. What
version
of gromacs are you using and what selection string are you using?
On Tue, Apr 3, 2018 at 11:32 AM, abhisek Mondal <abhisek.m...@gmail.com>
wrote:
Location of the files:
https://drive.google.com/drive/u/0/folders/0B6O-
L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan <e.jjorda...@gmail.com>
wrote:
Can you post the gro file and the resulting index file?
On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal <
abhisek.m...@gmail.com>
wrote:
Hi,
I'm just having some issue creating index file for umbrella
sampling.
I have a ligand:
Group 20 (NAP) has 73 elements
Now when I run following command:
gmx make_ndx -f npt.gro
and try to add NAP for index.ndx, only 6 elements were being added.
I don't understand the problem here.
NAP is clearly showing is of 73 elements, but how come it is
showing
me 6
elements when added to index file ?
Please help me out here.
Thanks.
--
Abhisek Mondal
*Senior Research Fellow*
*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*
*Kolkata 700032*
*INDIA*
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*CSIR-Indian Institute of Chemical Biology*
*Kolkata 700032*
*INDIA*
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Abhisek Mondal
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*Structural Biology and Bioinformatics Division*
*CSIR-Indian Institute of Chemical Biology*
*Kolkata 700032*
*INDIA*
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
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