Re: [gmx-users] Large system

2019-01-02 Thread Bratin Kumar Das 
Check the .itp files...it's possible that you forgot to delete atom number
from the last of the file

On Wed 2 Jan, 2019, 12:18 PM Anuj Ray  Sir,
>
> Since the array size of .gro/.pdb file for atom number is not greater than
> 5 digits, that's why if my system has >= 10 atoms then, it shows that
> no. of coordinates mismatch in .gro and .top file. Although the file
> corrected_wat_DMPC_18_32.pdb has 153216 coordinates, i get the following
> error.
>
> Command line:
>   gmx grompp -f minim.mdp -c corrected_wat_DMPC_18_32.pdb -p dmpctopol.top
> -o em.tpr
>
> Fatal error:
> number of coordinates in coordinate file (corrected_wat_DMPC_18_32.pdb,
> 9)
>  does not match topology (dmpctopol.top, 153216)
>
>
>
>
>
>
>
>
> On Wed, Jan 2, 2019 at 12:18 AM  wrote:
>
> > [image: Boxbe]  This message is eligible
> > for Automatic Cleanup! (pbusc...@q.com) Add cleanup rule
> > <
> https://www.boxbe.com/popup?url=https%3A%2F%2Fwww.boxbe.com%2Fcleanup%3Fkey%3DHrOF%252BjTOvp0Cf6CNxnGnxFFovz45l3r%252BVv684FrcTxU%253D%26token%3DuwjKuuWXMIOgCqLDQJs%252FZv5SDAdb6Oo%252Bo7D3WuJIGjbMuUsyDiNs2k0G1JlQwHvZp6LfurXxmiQ2kSU4i5Ul%252BRqdZmtveskcPfgAyNak2ctwu4ZCYxZu5xgUXI7o8%252F1Hw%252Fhsq6MhOVk%253D&tc_serial=46674948998&tc_rand=1281816478&utm_source=stf&utm_medium=email&utm_campaign=ANNO_CLEANUP_ADD&utm_content=001
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> >
> > As suggested,  compare the number of molecules/atoms implied in your top
> > file against that in your gro/pdb file.  This is one aspect of Gromacs
> that
> > it never gets wrong.
> >
> > -Original Message-
> > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> >  On Behalf Of Bratin
> > Kumar Das
> > Sent: Tuesday, January 01, 2019 5:22 AM
> > To: gmx-us...@gromacs.org
> > Subject: Re: [gmx-users] Large system
> >
> > There must be something wrong in your pdb or gro file. Give the proper
> > error
> > message. They way you told your problem..no one can understand.
> >
> > On 01-Jan-2019 11:41 AM, "Anuj Ray"  wrote:
> >
> > Respected Sir
> >
> > I am trying to prepare a minimization input file (.tpr) for a system
> having
> > 153216 atoms but the grompp command is reading only upto 9 atoms.
> What
> > is the procedure to prepare the input for such system?
> >
> > Regards
> > Anuj
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[gmx-users] ligand dissociation in gromacs

2019-01-02 Thread venkat 
Sir,
  i need to study Crystal complex structure (protein and ligand)
ligand dissociation by using md methods.  Is there any way perform in
gromacs like RAMD
if its there means kindly provide tutorial for that it will helpful for me.

Thank You.

Sincerely
S.venkatesh
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