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Hi,
if you were able to obtain a simulation it means you had a valid .top file!
In any case, gromacs recognises disulfide basing on the distance beween the
SG atoms.
In addition, the two chains are supposed to be in the same molecule.
So, my advice is, remove all the TER from pdb (but the last one)
Hi,
I am new to gromacs and started playing a bit on my laptop (Lenovo Y510,
Geforce 8400M GT) running ubuntu 12.10 with cuda 5.0.
Everything is working well, gromacs does not complain about anything.
But sometimes when using mdrun at start the gpu status is "insane". What
does that mean ?
Original Message
Subject: simulating only few residues from whole protein
From:preetichoudh...@iisermohali.ac.in
Date:Tue, March 19, 2013 10:45 am
To: gmx-users@gromacs.org
--
Thanks Francesco.
But my problem is exactly opposite. I do have a .top file containing
both chain linked by disulfide bridge. I ran the simulation. Now I
have extracted .xtc file for each chain separately and I want the
corresponding, separate .top file for each chain. when I separate the
pdb and r
Could you simply edit the file and removing the atom from [atoms] section ?
grompp wil complain regarding the line containing interactions. But also
these
few lines can be removed. Otherwise, vmd has the TopoTools that write the
.top
topology of the loaded pdb. Unfortunately, this topologyes are no
I did it. Simply I changed the name of Cys which forms interchain
dsiulfide bond to CYS2 in the separated pdb file and I used G43a1
forcefeild to run pdb2gmx. This gives a topology with same number of
atom which is present in .xtc file. CYS2 is present .rtp file of G43a1
forcefeild probably to form
If it works then you are right :)
2013/3/19 shahid nayeem
> I did it. Simply I changed the name of Cys which forms interchain
> dsiulfide bond to CYS2 in the separated pdb file and I used G43a1
> forcefeild to run pdb2gmx. This gives a topology with same number of
> atom which is present in .xt
Anyone tell me how do I freeze the particular residues in NPT-NVT equillibrium
steps ? I want them in same conformation as pdb for further production run ?
Thanks in advance --
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the
Thanks. So in this case no matter what density I will start with e.g.
480 kg/m3 presuming the force filed is correct I should get at given
conditions the density of interest?
Steven
On Mon, Mar 18, 2013 at 10:34 PM, Justin Lemkul wrote:
>
>
> On 3/18/13 6:14 PM, Steven Neumann wrote:
>>
>> On Mo
On 3/19/13 5:52 AM, Steven Neumann wrote:
Thanks. So in this case no matter what density I will start with e.g.
480 kg/m3 presuming the force filed is correct I should get at given
conditions the density of interest?
If the force field has been parametrized to reproduce the density, then yes
On 3/19/13 5:44 AM, 라지브간디 wrote:
Anyone tell me how do I freeze the particular residues in NPT-NVT equillibrium
steps ? I want them in same conformation as pdb for further production run ?
Thanks in advance
Use freezegrps or strong position restraints.
-Justin
--
On 3/19/13 4:13 AM, preetichoudh...@iisermohali.ac.in wrote:
Original Message
Subject: simulating only few residues from whole protein
From:preetichoudh...@iisermohali.ac.in
Date:Tue, March 19, 2013 10:45 am
To: gmx-use
Dear Justin Thank you for your Previous Reply
I am
following you Protein Lipid Tutorial . In Analysis Part I Have Done Deuterium
Order Parameters Analysis using index files . Kindly brief About Deuterium
order paramete
On 3/19/13 6:59 AM, vidhya sankar wrote:
Dear Justin Thank you for your Previous Reply
I am
following you Protein Lipid Tutorial . In Analysis Part I Have Done Deuterium
Order Parameters Analysis using index files .
Hi,
I know this question has been asked for a few times already but I don't seem
to get it. :(
I did:
1) editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt dodecahedron
2) genbox -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top
3) grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
On 3/19/13 7:44 AM, Ewaru wrote:
Hi,
I know this question has been asked for a few times already but I don't seem
to get it. :(
I did:
1) editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt dodecahedron
2) genbox -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top
3) grompp -f ions.mdp -
HI Justin,
Thanks for the prompt reply! :) Correct me if I'm wrong, but I thought the
protein has to be in the center (inside the box) before the simulation, is
it?
Thank you.
Best regards.
--
View this message in context:
http://gromacs.5086.n6.nabble.com/trjconv-centre-protein-tp5006454
On Mar 19, 2013, at 11:45 AM, Justin Lemkul wrote:
On 3/19/13 5:44 AM, 라지브간디 wrote:
Anyone tell me how do I freeze the particular residues in NPT-NVT
equillibrium steps ? I want them in same conformation as pdb for
further production run ? Thanks in advance
Use freezegrps or strong posi
On 3/19/13 8:00 AM, Ewaru wrote:
HI Justin,
Thanks for the prompt reply! :) Correct me if I'm wrong, but I thought the
protein has to be in the center (inside the box) before the simulation, is
it?
Absolutely not. In a periodic system, there is no such thing as a center.
Centering within
Crystal clear! Thank you Justin! :)
Take care.
Regards.
--
View this message in context:
http://gromacs.5086.n6.nabble.com/trjconv-centre-protein-tp5006454p5006459.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
--
gmx-users mailing listgmx-users@gromacs.org
ht
Greetings,
I am relatively new to MD, and I am attempting to simulate a metal-organic
framework but I don't seem to be even able to get past the energy minimization
phase. I could appreciate any insight into what I might be doing wrong. Here is
a brief summary of what I have done:
- constructe
On Tue, Mar 19, 2013 at 9:16 AM, Jeff Woodford <
jwoodf...@missouriwestern.edu> wrote:
> Greetings,
> I am relatively new to MD, and I am attempting to simulate a metal-organic
> framework but I don't seem to be even able to get past the energy
> minimization phase. I could appreciate any insight
Dear Users
I am using groamcs 4.4.4 and when I run grompp during equilibration process, it
closes with error
" Fatal error:Topology include file "posre_Protein.itp" not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentati
Dear Gromacs user,
I was having a question on when need to use jacobian coorection of -2KTln(r)
( gromacs manual chapter 6) term when calculating PMF. I understand for a
3-dimensional radial coordinate like distance between two groups, this term
need to taken care of. But, if the PMF is comput
Dear users,
I modified my top file, because I didn't want some bonds. So I deleted them and
changed charges on some atoms.
I want to go on with such a top file, however I am not sure that these changes
are implemented properly or not. Would you please let me know if what I did is
right or n
On Tue, Mar 19, 2013 at 10:46 AM, Kshatresh Dutta Dubey wrote:
> Dear Users
>
> I am using groamcs 4.4.4 and when I run grompp during equilibration
> process, it closes with error
> " Fatal error:Topology include file "posre_Protein.itp" not found
> For more information and tips for troubleshoot
On Tue, Mar 19, 2013 at 1:07 PM, Shima Arasteh
wrote:
>
>
> Dear users,
>
> I modified my top file, because I didn't want some bonds. So I deleted
> them and changed charges on some atoms.
> I want to go on with such a top file, however I am not sure that these
> changes are implemented properly
:)
In fact, I have a NMR pdb file of a cyclic peptide. To get a proper gro and
topology files, I ran pdb2gmx without -ter flag. Then tried to modify the top
file. Is there any better ideas?
Thanks for your reply.
Sincerely,
Shima
From: Justin Lemkul
To: Shi
Would you please let me know if it is acceptable to add dihedrals and angles
and bonds? and not to add any pairs to the top? just deleting the pairs which
are added by pdb2gmx incorrectly to the terminus?
And I don't know that if I don't add all bonds or dihedrals what would happen?
How would
On Tue, Mar 19, 2013 at 1:36 PM, Shima Arasteh
wrote:
> Would you please let me know if it is acceptable to add dihedrals and
> angles and bonds? and not to add any pairs to the top? just deleting the
> pairs which are added by pdb2gmx incorrectly to the terminus?
>
>
> And I don't know that if I
Thank you! This is a very good suggestion.
On Mon, Mar 18, 2013 at 11:49 PM, Dr. Vitaly Chaban wrote:
> > Hi!
> > I would like to simulate halkali halides in GROMACS by using the
> Tosi-Fumi
> > potential.
> >
> > The potential is of this kind (Born Mayer Huggins), with an exponential,
> a
> > 6
Dears,
There is term of function for each 4 atoms in dihedral section in top file. How
this function is defined? To add extra dihedrals manually, I need to add
function too.
Thanks.
Sincerely,
Shima
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo
As I found up to now, func 2 is related to improper dihedrals. How can I find
improper dihedrals? Can I not add them?
Sincerely,
Shima
- Original Message -
From: Shima Arasteh
To: Discussion list for GROMACS users
Cc:
Sent: Tuesday, March 19, 2013 9:46 PM
Subject: [gmx-users] Func
On Tue, Mar 19, 2013 at 2:16 PM, Shima Arasteh
wrote:
>
>
> Dears,
>
> There is term of function for each 4 atoms in dihedral section in top
> file. How this function is defined? To add extra dihedrals manually, I need
> to add function too.
>
>
All of this information is in the manual, Chapters
Dear gromacs users
I have performed MD simulation using Tip4p/ice model, which is copied from
[http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_topology_file_for_the_TIP4P/Ice_model]
The MD actually works and the output structure looks fine.
However, after 11ns run, the run was suddenly sto
On 3/19/13 9:58 PM, Kenji Mochizuki wrote:
> Dear gromacs users
>
> I have performed MD simulation using Tip4p/ice model, which is copied from
> [http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_topology_file_for_the_TIP4P/Ice_model]
>
> The MD actually works and the output structure looks
I follow your advice to edit the bond conditions of residues Fbg and Fen in
my rtp file. Subsequently, I should modify the hdb file to add hydrogens for
Fbg and Fen. However, I get the fatal error message " Atom +C1 not found in
residue Fbg 113, rtp entry Fbg while adding hydrogens." I can successf
Dear Eb,
Thanks for the reply and input! I have posted part of the bonded itp file
as below. Could you please be kind to specify how to revise the
multiplicity? Many thanks! BTW, the force field we used is Amber. Thanks
again!
Cheers
Jeremy
--
[ dihedraltypes ]
;i
FYI, I only showed you the bond part of the residue in the previous email
(since that was the section I was commenting on and showed how it should be
there) there should be some atom details prior to that, as required by the rtp
format. You need to use your own judgment and the manual to ensure
Hi Jeremy,
I have checked how improper dihedral should look like in Amber, guessing that
you used amber99sb force field. But I am wondering from where the improper in
your ligand.itp was generated. As it doesn not look alike with the amber force
field. It actually is not the problem of multipli
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