On 4/16/13 9:07 AM, Group Gro wrote:
Dear GROMACS users,
Hi.
I want to study different protein-drug complexes and I follow the procedure
mentioned in the
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/.
I copied and pasted the positions of each drug to the end
se topics are discussed routinely.
-Justin
Thanks alot.
ali kazemi
department of biochemistry
islamic azad university shahrekord branch
*From:* Justin Lemkul
*To:* Group Gro ; Discussion list for GROMACS users
*Sent:
On 2/25/13 6:09 AM, Group Gro wrote:
Dear Gromacs Users.
I apologize for asking a question that has come up several times by numerous users in the
previous e-mails, but I have read the answers and suggestions to those posts and I am not
still able to solve the problem based on them. It i
Przemek Bartha wrote:
Dear gmx users,
my goal is to aquire a PMF courve of two amino-acids (ASP and LYS) of
which one is pulled from the other. I followed Justin's tutorial on
umbrella sampling.
Here are the results.
profile.xvg:
http://przemekbartha.pl/upload/profile.png
histo.xvg:
http://p
ITHAYARAJA wrote:
Dear Sir,
Greetings!
I found the following error while preforming pdb2gmx command,
Fatal error:
Incomplete ring in HIS-3
You have an incomplete starting structure. In order for pdb2gmx to work, you
need an intact coordinate file. If your input is a .pdb file, it may
- Original Message -
From: leila separdar
Date: Sunday, November 21, 2010 19:15
Subject: Re: [gmx-users] request
To: Discussion list for GROMACS users
>
> hi
> do I need any .pdb file for making .gro and .top file?
>
> I make .pdb file with hyperchem software
hi
do I need any .pdb file for making .gro and .top file?
I make .pdb file with hyperchem software and then I used pdb2gmx command in
order to make .gro and .top files. but I think my way is wrong. is it true?
is there anybody that done this simulation?
leila
On Sun, Nov 21, 2010 at 11:24 A
Hi,
Define an itp file which has the non-bonded info. Then define a mdp (md
parameter file) and also make a structure file (gro). Also you need a
topology file (top) which corresponds to the structure file.
You will have to do some background work. Manual should be your friend.
amit
On Sat, Nov
[EMAIL PROTECTED] wrote:
Is it possible for the moderators to change some setting that
would automatically word-wrap all posts on the mailing list
archive?
This would be a good thing. It is also normally possible to set your own
word wrap in an email client.
Mark
Chris,
>Right. I remember looking into this at one point, and I don't think
>the manual is correct; it looks to me like dihres.c handles
>periodicity properly. In particular, there is the followign comment in
>dihres.c:
It's good to see that this is actually a comment in the source code, I didn
Chris,
I have included my .top file. The relevant section is in [ dihedral_restraints ]
This file is a template that I use like this:
sed 's/PHI/${phi_value}/' template.top | sed 's/PSI/${psi_value}/' >
phi${phi_value}_psi${psi_value}.top
Just out of curiousity, which GROMACS version are you
Chris,
I'll have to assume you know what you're doing with using impropers to
calculate PMFs. I've done this using the dihedral restraints code.
Have you double-checked that? That's the first place I would look.
Otherwise, I don't have a great test system for you.
David
On 4/25/07, Chris Neal
David Konerding wrote:
Hi
I was happy to see the 'Speeding up Parallel GROMACS' paper. I'd like
to try
the GROMACS patch for better all-to-all, as well as the all-to-all test
program referred
to on the paper. I can't find it on the GROMACS site.
Hi David,
you can download both at
www.grom
hadi behzadi wrote:
Program grompp, VERSION 3.3
Source code file: topio.c, line: 385
Fatal error:
Invalid order for directive moleculetype, file ""1.top"", line 17
The line 17 is [ moleculetype ].
As it says, this directive is out of order. You have to #include some
forcefield files first, whi
>Fatal error:
>Invalid order for directive moleculetype, file ""1.top"", line 17
>The line 17 is [ moleculetype ].
>I request you all to give suggestion for this.
Go to www.gromacs.org, click on the link that says search, which will
take you to http://www.gromacs.org/external/search.html
In the
In God We Trust
Hello
Here is your topology. Thank you very much in
advanceKarim MahnamInstitute of Biochemistry and
Biophysics (IBB)Tehran University P.O.box 13145-1384Tehran
Iran http://www.ibb.ut.ac.ir/
-Original
Message-From: hadi behzadi <[EMAIL PROTECTED]>To:
gmx-users@groma
hadi behzadi wrote:
hello
I have a topology file for propanol as is in below , how we can obtain
topology file for 100 molecule of propanol
thanks
chapter 5
are you sure you want this force field by the way?
in the systems section write
drg 100
;
;
; This file was gen
Mikko Hellgren wrote:
>
> Hi all Gromacs users and developers, I wonder if anybody has pdb files
> for NAD+ (NADH in Gromacs), NADH (NADP) and Retinol (RTOL) with the same
> labels as in Gromacs topologies. This would save me a lot of time in my
> work since the atom names in my PDB for the ligan
Mobley <[EMAIL PROTECTED]>
Date: Tuesday, March 28, 2006 5:30 pm
Subject: Re: [gmx-users] Request for PDB with the same label as in
Gromocs topologies.
To: [EMAIL PROTECTED], Discussion list for GROMACS users
> Mikko,
>
> If I understand correctly what you're asking (that is, what at
Mikko,
If I understand correctly what you're asking (that is, what atom types
in GROMACS correspond to what names in the PDB) this is really
nontrivial and there isn't one answer. In particular, each force field
has its own set of atom types. There are, for example, many different
types of carbon
20 matches
Mail list logo
