[gmx-users] Doubt in nmol tool

Dear Gromacs users, Can anyone explain about -nmol (number of molecules ) option in gmx gyrate tool. According to me I have 3 peptide chains in my simulation box and I am using " -nmol 3". Is it correct what I have used for this option? Regards Sundari -- Gromacs Users mailing list * Please se

Re: [gmx-users] Doubt in nmol tool

What do you want? Do you want to calculate the radius of gyration of the three chain at a time? If so then make a index of these protein chains together and calculate rg by selecting it. If not then calculate the chain's rg individually. -Soham On Mon, 8 Apr 2019, 2:36 pm Sundari, wrote: > Dear

Re: [gmx-users] Doubt in nmol tool

I want to to calculate Rg of whole protein in the simulation box at a time not the individual chains. And for this I have selected Rg for "C-alpha" atoms plus "-nmol 3" . Thank You, Sundari On Mon, Apr 8, 2019 at 2:50 PM Soham Sarkar wrote: > What do you want? > Do you want to calculate the ra

Re: [gmx-users] Doubt in nmol tool

In that case select all c-alpha and make a group in index.ndx and run gmx gyrate for this group only and you are done. On Mon, 8 Apr 2019, 3:09 pm nidhi, wrote: > I want to to calculate Rg of whole protein in the simulation box at a time > not the individual chains. > And for this I have selecte

Re: [gmx-users] Doubt in nmol tool

That means there is no need of using -nmol option. Thank You very much :) On Mon, Apr 8, 2019 at 3:57 PM Soham Sarkar wrote: > In that case select all c-alpha and make a group in index.ndx and run gmx > gyrate for this group only and you are done. > > On Mon, 8 Apr 2019, 3:09 pm nidhi, wrote:

Re: [gmx-users] Doubt in nmol tool

No need to use -nmol On Mon, 8 Apr 2019, 4:21 pm nidhi, wrote: > That means there is no need of using -nmol option. > > Thank You very much :) > > > On Mon, Apr 8, 2019 at 3:57 PM Soham Sarkar wrote: > > > In that case select all c-alpha and make a group in index.ndx and run gmx > > gyrate for

[gmx-users] question

*hello* *How can I position restraint cofactor and ligand **together?* -- 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 r

[gmx-users] question

*hello* *How can I position restraint cofactor and ligand **together?* -- 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 r

Re: [gmx-users] Doubt in nmol tool

Dhanyavad!! On Mon, 8 Apr 2019, 16:34 Soham Sarkar, wrote: > No need to use -nmol > > On Mon, 8 Apr 2019, 4:21 pm nidhi, wrote: > > > That means there is no need of using -nmol option. > > > > Thank You very much :) > > > > > > On Mon, Apr 8, 2019 at 3:57 PM Soham Sarkar wrote: > > > > > In th

Re: [gmx-users] question

Hi You need to create the restrain file of co-factor and ligand separately. Next you have to include the restrain file in the topolog file. Check the gromacs manual On Mon 8 Apr, 2019, 5:22 PM m mar *hello* > > *How can I position restraint cofactor and ligand **together?* > -- > Gromacs User

Re: [gmx-users] Pulling simulation

Hi Naveen, I think you are looking for absolute reference position in space, which is mention on page 436 of manual 2019.1 In my case, I pull ACE residue. my pulling code is: pull= yes pull_ncoords= 1 ; only one reaction coordinate pull_ngroups= 1

Re: [gmx-users] No default Bond types error despite entry in ffbonded.itp

Hi, Thanks for the input. I’m just trying to get it to run at this point — I’ll worry about the box later. Could you please elaborate on “you haven’t mentioned those entries in the right way”? The names of the atoms are correct, it’s listed correctly under [ bondtypes ], and the parameters are

Re: [gmx-users] No default Bond types error despite entry in ffbonded.itp

On Mon, Apr 8, 2019 at 7:26 PM Irem Altan wrote: > Hi, > > Thanks for the input. I’m just trying to get it to run at this point — > I’ll worry about the box later. > > Could you please elaborate on “you haven’t mentioned those entries in the > right way”? The names of the atoms are correct, it’s

[gmx-users] order of atoms in the index file

Hello all, I am trying to calculate the dihedral angels of a group of atoms in a molecule. As I am only interested in part of the molecule, I have manually made an index file containing the desired atoms in groups using gmx make_ndx. Yet, the atom's number in each group is in ascending order. M

Re: [gmx-users] MD of ligand-only system

Since you already have the .itp and .pdb then you simply construct your simulation box, run the energy minimisation etc steps then your production run. From the point at which you are currently, of having the topology and coordinate file, it is the same as for any other simulation (including prote

Re: [gmx-users] MD simulation of ligand only system

http://manual.gromacs.org/documentation/current/user-guide/run-time-errors.html#invalid-order-for-directive-xxx Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@mon

Re: [gmx-users] g_density problem

Typically selections are done by typing from the keyboard after the script has been run. However, since you appear to be submitting it to a cluster (using qsub) then the selections need to be done from the command line. See http://manual.gromacs.org/documentation/2019-beta1/onlinehelp/selections.

Re: [gmx-users] Pulling simulation

thank you so much @Quyen Vu. I'll get back to you soon. On Mon, Apr 8, 2019 at 7:00 PM Quyen Vu wrote: > Hi Naveen, > I think you are looking for absolute reference position in space, which is > mention on page 436 of manual 2019.1 > In my case, I pull ACE residue. > my pulling code is: > pull