Hi Shima,
You need to give a reference structure with the -s option. Otherwise the
program assumes you mean to use topol.tpr, which isn't present.
Cheers,
Tsjerk
On Sun, Jul 7, 2013 at 11:51 AM, Shima Arasteh
shima_arasteh2...@yahoo.comwrote:
Dear gmx users,
I' d like to get pdb files
Dear Shima
What is the name of your .tpr file?
If you had not chosen any name for it, Gromacs will generate a
topol.tpr for you and in my idea this error will not occur,
if not, you have to mention your file (e.g. Filename.tpr) explicitely
in your command line!
I hope this help you
Best
On Sun,
On 4/01/2012 12:30 PM, Peter C. Lai wrote:
I used VMD to process a gro file and wrote it to pdb, because VMD can't
write gro files. Because the # of residues exceeds , it numbered the
remaining residues in the PDB in 4 bit hex. Editconf will not convert the
hex numbered residue ids back to
On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote:
On 4/01/2012 12:30 PM, Peter C. Lai wrote:
I used VMD to process a gro file and wrote it to pdb, because VMD can't
write gro files. Because the # of residues exceeds , it numbered the
remaining residues in the PDB in 4 bit hex.
On 4/01/2012 1:07 PM, Peter C. Lai wrote:
On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote:
On 4/01/2012 12:30 PM, Peter C. Lai wrote:
I used VMD to process a gro file and wrote it to pdb, because VMD can't
write gro files. Because the # of residues exceeds , it numbered the
remaining
On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote:
On 4/01/2012 1:07 PM, Peter C. Lai wrote:
On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote:
On 4/01/2012 12:30 PM, Peter C. Lai wrote:
I used VMD to process a gro file and wrote it to pdb, because VMD can't
write gro files. Because
On 4/01/2012 2:19 PM, Peter C. Lai wrote:
On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote:
On 4/01/2012 1:07 PM, Peter C. Lai wrote:
On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote:
On 4/01/2012 12:30 PM, Peter C. Lai wrote:
I used VMD to process a gro file and wrote it to pdb, because
On 2012-01-04 02:54:28PM +1100, Mark Abraham wrote:
On 4/01/2012 2:19 PM, Peter C. Lai wrote:
On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote:
On 4/01/2012 1:07 PM, Peter C. Lai wrote:
On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote:
On 4/01/2012 12:30 PM, Peter C. Lai wrote:
I
On 4/01/2012 2:59 PM, Peter C. Lai wrote:
On 2012-01-04 02:54:28PM +1100, Mark Abraham wrote:
On 4/01/2012 2:19 PM, Peter C. Lai wrote:
On 2012-01-04 01:21:01PM +1100, Mark Abraham wrote:
On 4/01/2012 1:07 PM, Peter C. Lai wrote:
On 2012-01-04 12:46:09PM +1100, Mark Abraham wrote:
On
...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] pdb files
To: gurbulako...@yahoo.com, Discussion list for GROMACS users
gmx-users@gromacs.org
Date: Saturday, March 7, 2009, 9:28 AM
oguz gurbulak wrote:
Dear All,
I want to use packmol pdb files
...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] pdb files
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Thursday, March 12, 2009, 12:11 PM
oguz gurbulak wrote:
Dear Justin,
Can I get a itp file tempate for OPLS-AA according to your suggestions
Thanks in advance
--- On *Thu, 3/12/09, Justin A. Lemkul /jalem...@vt.edu/* wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] pdb files
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Thursday, March 12, 2009, 12:11 PM
oguz gurbulak
oguz gurbulak wrote:
Dear All,
I want to use packmol pdb files that includes one or two different types
of molecules. And I seached Gromacs manuals, tutorials and mail archives
in order to have enough information about using packmol pdb files in
Gromacs. But I couldn't find any
Sagittarius wrote:
Dear Gromacs users,
Could you please help me to find pdb files for
glyceric acid esters
cyanamide
phosphatidylcholine
glyceroyl thioesters
tetrose
polyglyceric acid
hemiacetal
Thank you in advance
You build these yourself using a molecule building program. I don't know
Dear Mark Abraham
Thank you very much for your help.
Could you please help me to find such a not free molecule building program.
Maybe it will be useful anyway somehow.
Thank you in advance.
Mark Abraham [EMAIL PROTECTED] wrote:
Sagittarius wrote:
Dear Gromacs users,
Could you
Dear Mark Abraham
Thank you very much for your help.
Could you please help me to find such a not free molecule building
program.
Maybe it will be useful anyway somehow.
Start with a Google search.
Mark
___
gmx-users mailing list
This site can have some:
http://alpha2.bmc.uu.se/hicup/
Welcome to HIC-Up, the Hetero-compound Information Centre - Uppsala, a
freely accessible resource for structural biologists who are dealing
dealing with hetero-compounds (small molecules).
Catch ya,
Dr. Dallas Warren
Lecturer
Department
Dallas B. Warren wrote:
This site can have some:
http://alpha2.bmc.uu.se/hicup/
Welcome to HIC-Up, the Hetero-compound Information Centre - Uppsala, a
freely accessible resource for structural biologists who are dealing
dealing with hetero-compounds (small molecules).
otherwise molden or
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