On Thu, Apr 4, 2013 at 11:40 AM, Anna Marabotti wrote:
> Dear gmx-users, dear Mark,
> thank you for all the help you are giving me for this subject. I'm still
> proceeding to my target..
> Thanks to your previous suggestions, I was able to parametrize bonds and
> angles of CFY. Now I'm dealing wi
Dear gmx-users, dear Mark,
thank you for all the help you are giving me for this subject. I'm still
proceeding to my target..
Thanks to your previous suggestions, I was able to parametrize bonds and
angles of CFY. Now I'm dealing with dihedrals...
In the parameter files derived by Antechamber
On 1/22/13 2:02 PM, Tom wrote:
Thanks a lot, Justin!
I names residue names to match the force field's expectations
But I am still having problem of using amber03.ff.
This my pdb file:
_
.
ATOM 28 H5DC5 1 2.443 -4.389 1.332 1.00 0.00 H
*ATOM 29 P
On 1/8/13 12:06 PM, Tom wrote:
Table 5.5 does list the option of use harmonic type potential for improper
dihedral. (f. tp =5)
It's function type 2.
But I am confused how to build this on the ffbond.itp file and manu is not clear
about this.
You would define the interaction in ffbonded.i
Table 5.5 does list the option of use harmonic type potential for improper
dihedral. (f. tp =5)
But I am confused how to build this on the ffbond.itp file and manu is not
clear about this.
Do you think that in the case of OPLS AA, the periodic improper dihedral is
the ONLY option?
Thanks a lot fo
On 1/8/13 10:34 AM, Tom wrote:
Thanks for your reply, Justin!
I knew that gmx use as the follows for opls aa:
; Improper OPLS dihedrals to keep groups planar.
; (OPLS doesnt use impropers for chiral atoms).
; Since these functions are periodic of the form 1-cos(2*x), they
Thanks for your reply, Justin!
I knew that gmx use as the follows for opls aa:
; Improper OPLS dihedrals to keep groups planar.
; (OPLS doesnt use impropers for chiral atoms).
; Since these functions are periodic of the form 1-cos(2*x), they are
actually
; implemented as prope
They have also the complete force field parameters under:
OPLS Auxiliary topologyoplsaaff.itp
if there are more paramters then in the oplsaa.ff directiory, then they
have probably developed these parameters.
They give this paper as a reference for the calculations. Probably
something is
On 31/08/2012 1:03 PM, klexa wrote:
>>
If I recall correctly, the residue number printed by pdb2gmx is
actually the
residue index (starting from zero), so the problematic residue is MLE,
which
does have CB.
Good thought, but the index here starts counting from 1 (and has done so
for at le
>>
If I recall correctly, the residue number printed by pdb2gmx is actually the
residue index (starting from zero), so the problematic residue is MLE, which
does have CB.
-Justin
Hi Justin,
Thank you for the fast response. That makes sense, but the problematic
residue is actually both
Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private help service. I am CC'ing the list and would ask that anything
further be posted there.
Before posting anything to the list, check the list archive. Your problem has
been posted and answered literally
For building membrane/protein systems I recommend charmm-gui.org
The server automatically builds the coordinates, which you should be
able to use
with any modeling program; CHARMM equilibration scripts are generated
as well
Krzysztof
On 9/2/10 6:20 AM, Justin A. Lemkul wrote:
Please kee
Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private help service. I am CC'ing the message there; please continue any
discussion via the forum.
Creating a lipid bilayer is not a particularly easy task. You can generate a
leaflet by replicating the coord
Hi there,
I didn't have time to improve opls generation in ACPYPE. I need to put a
Wiki about it for the moment, but to get the Opls atomtypes, use MKTOP:
http://labmm.iq.ufrj.br/mktop/
Good luck,
Alan
On Tue, Jul 20, 2010 at 14:42, wrote:
> Hello all
>
> I want to study protein-ligand using
Hi Emily,
I have no idea about your problems, but I noticed that the gromacs you
used might be the one my colleague had sent to you, he modified
something to fit my multicores processors, I guess you may do a try to
use the original and official one also.
Good luck,
Lina
>
Hi Pavan,
Please, I'm not a user list. This is in no way attached to the
tutorials of mine.
But your problem arises because you're mixing things up. You're using
a new run input (.tpr) file, and a checkpoint (.cpt) file. Either you
continue runs using checkpoint files (preferred) or you generate
You will have to set the right environment variable for CFLAGS to get
debug symbols:
cd gromacs_directory
CFLAGS="-O0 -g3"
./configure
might do the trick.
you can use gdb to check whether there are debug symbols in an executable.
Alex
Inon Sharony schrieb:
>
> reply to:
> http://lists.gromac
reply to:
http://lists.gromacs.org/pipermail/gmx-users/2009-September/045006.html
"...
My usual advice is to compile GROMACS with -g, get a graphical
debugger(Totalview, ddd, insight, whatever) and spend a day stepping through
ashort mdrun to get some understanding about what is r
Hi,
With regards to the question about my tutorial, you have not taken care to
update your topology through the steps of preparing the system. Using the -p
flag with genbox and genion will make these changes for you, as is instructed in
the tutorial.
With regards to your other question, pl
Hi,
Actually the xdrfile_xtc.h file did include the xdrfile.h. And I also tried
to include xdrfile_xtc.h directly in my source file. The link error is still
there. I really don't know what's the problem because the make test command
passed.
On Mon, Aug 17, 2009 at 1:34 PM, Vitaly V. Chaban wrote
Hi,
1. It seems you also need to include xdrfile.h.
2. Are the library files located in the same directory with your
source files when you link?
VItaly
>
> Recently I am trying to use the xdr library downloaded from gromacs org to
> read xtc files. However when I link my program with the library
Ragnarok sdf wrote:
I have tried with decane, octane and CCl4. The three of them got me
the same problem, pressure scaling more than 1%. I have tried
increasing the tau_p value, cause that was one of the solutions given
in gmx user's list. That didn´t work out either. All my simulations
were ca
I have tried with decane, octane and CCl4. The three of them got me
the same problem, pressure scaling more than 1%. I have tried
increasing the tau_p value, cause that was one of the solutions given
in gmx user's list. That didn´t work out either. All my simulations
were carried out using ffgmx fo
>Hello, I would like to know if there is any recommendation onto
>setting up a system with a protein in a apolar solvent box. If there
>is any tutorial or web page with topologies for solvents. I read that
>the decane box that comes with gromacs is not to be used for
>simulations, if that is true,
Anna Marabotti wrote:
Dear Justin,
I hope you wouldn't mind if I contact you directly, but I think I cannot send
you the requested .log file via
the gmx-users list because the message would be filtered.
It is best to keep the discussion on the list; posting short .mdp files (pasted
into the
Julio Benegas wrote:
Dear David,
We are sorry to bother you on perhaps a simple question, but elusive to us.
We want to run a MD simulation of three units of chitosan.
We are using Gromacs ffG53A6 force field and we can not find in the
corresponding library the parameters corresponding to the NH2
vivek sharma wrote:
HI justin,
Thanks for reply. It is well understood that the energy minimization
step will minimize energy, but what is the purpose of MD (after EM and PR)?
please reply
Again, please keep all Gromacs-related correspondence on the gmx-users list.
The purpose of MD? Inte
vivek sharma wrote:
Hi Justin,
I think my query is very basic regarding GROMACS, so I am mailing you
individually instead of using mailing list.
Basic or not, please keep all Gromacs-related correspondence on the gmx-users
list.
My query is ...
How does gromacs proceed ?
On what basis (pa
chemical chemical calculation or use equivalent
parameters. (but this is more a topic for the amber mailing list...)
kind regards,
servaas
Message: 6
Date: Mon, 31 Mar 2008 10:25:17 -0400
From: "Xiangyu Fan" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Re: Help needed on using gen
Hi Servaas,
Thanks for your reply. Your inforamtion is very helpful. Now I am trying to
write the topology file by myself when dealing with a small molecule. I
have know their conversion relationship, but in my case, I want to fix a few
atoms in a plane. From the gaff.dat file , I can see the pa
I don't think you can generate your topology from the pdb file with
gromacs in this case (with gaff). You can first make it in amber and
than convert it to gromacs.
On this website is the info you need, in the FAQs there is a link to
dowload the script to do the job.
http://chemistry.csulb.edu/ffam
Quoting mahendra awale <[EMAIL PROTECTED]>:
> hi
>
> dear sir
>
> i am mahendra awale doing M.S in NIPER INDIA in pharmacoinformatics
> i am running MD simulation
> i have a problem while running MD would u please help me
It is best to keep Gromacs-related questions on the users' list, and I am
c
Hello, Tawhid
In the file pull.ppa, you can appoint a direction to pull
And if you want to pull some atoms together, you can make them in one same
group in the *.ndx file and give them a name like ‘pull'. And then, put the
'pull' in group_1 .
Li Zhenhai
Department of Engineering Mechanics
Tsin
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