Re: [gmx-users] Convert gro into psf

[Justin Lemkul]

On 5/10/16 11:12 AM, Roshan Shrestha wrote:

Thanks Justin, I will surely look into it. But, if I do want to work
through Gromacs instead, am I going through write path with the above
command.



Start here:

http://www.gromacs.org/Documentation/Tutorials

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Convert gro into psf

[Roshan Shrestha]

Thanks Justin, I will surely look into it. But, if I do want to work
through Gromacs instead, am I going through write path with the above
command.
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Re: [gmx-users] Convert gro into psf

[Justin Lemkul]

GROMACS tools do not read or write PSF.  If you want to use NAMD, there are 
other forums for that (namely, their mailing list).  You can generate the PSF 
using CHARMM, CHARMM-GUI, VMD, etc.


-Justin

On 5/9/16 11:23 PM, Roshan Shrestha wrote:

I am extremely sorry that I did not provide full command, the command is-
gmx pdb2gmx -f 6pti.pdb -o bpti.gro -p topol.top -ignh -v where I chose
charmm27 for force field and tip3p for water model.
On 10 May 2016 8:39 am, "Roshan Shrestha"  wrote:


Is it possible to convert .gro file into. psf file ?
I am finding it tough to create psf file for 6pti.pdb using NAMD. So, Can
I convert say bpti.gro into bpti.psf where I produced bpti.gro using
command gmx pdb2gmx -f 6pti.pdb -o bpti.gro -p



--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Convert gro into psf

[Roshan Shrestha]

I am extremely sorry that I did not provide full command, the command is-
gmx pdb2gmx -f 6pti.pdb -o bpti.gro -p topol.top -ignh -v where I chose
charmm27 for force field and tip3p for water model.
On 10 May 2016 8:39 am, "Roshan Shrestha"  wrote:

> Is it possible to convert .gro file into. psf file ?
> I am finding it tough to create psf file for 6pti.pdb using NAMD. So, Can
> I convert say bpti.gro into bpti.psf where I produced bpti.gro using
> command gmx pdb2gmx -f 6pti.pdb -o bpti.gro -p
>
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[gmx-users] Convert gro into psf

[Roshan Shrestha]

Is it possible to convert .gro file into. psf file ?
I am finding it tough to create psf file for 6pti.pdb using NAMD. So, Can I
convert say bpti.gro into bpti.psf where I produced bpti.gro using command
gmx pdb2gmx -f 6pti.pdb -o bpti.gro -p
-- 
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