Hello,
What program are you using in AmberTools?
Try this in VMD
>> vmd prmtop_file_name -rst7 co-ordinate_file_with_no_of_atoms_on_top
I think, this should work.
If not, then try these -
*solution-1File with total numbers on top is called restart file. We can
use cpptraj to convert into crd file. This cpptraj command will output
coordinate file without total number on top. >> cpptraj -p prmtop_file_name
-y co-ordinate_file_with_no_of_atoms_on_top -x file.crd*
*solution -2*
>> sed -i '2d' crd_file # This command will delete first two lines.
Pancham
On Wed, Feb 21, 2018 at 7:17 PM, Stefano Guglielmo <
stefano.guglielmo.unito.it> wrote:
> Dear AMBER users,
> I generated topology and coordinates for a drug-like molecule using
> Ambertools 16; all seems to have gone ok, but as I try to open prmtop and
> prmcrd in VMD the geometry of the molecule is completely altered because
> VMD reads the first number in prmcrd file (i.e. the number of atoms in the
> molecule) as a coordinate: manually deleting the number solves the problem
> of visualization. Is there a workaround different from manually deleting
> the number of atoms in coord file? Or eventually is it possible to delete
> the number without encountering any issues?
> I am using VMD 1.9.3.
> Thanks in advance
> Stefano
>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> 10125 Turin, ITALY
> ph. +39 (0)11 6707178
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>
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Received on Thu Feb 22 2018 - 07:00:03 PST
