On 29/07/2012 5:11 PM, vidhya sankar wrote:
Dear justin,
Thank you for your previous reply.
Is there is any Thumb rule in setting rcoulomb ,
rvdw & rlist ?
Yes, use settings that have been proven to work with your forcefield
Dear Gromacs Users!
I want to analyze protein-ligand polar interactions by means of g_hbond utility
In particular I want to obtain some map wich include information
aabout dynamics of the h bonds occurence between defined polar groups
of the protein ( active site) and ligand polar atoms. For tha
I listened to you absolutely and didn't proceed any other way! What I created
in .rtp file for FVAL ( like what you described sometime ago), is as below:
First of all added the FVAL to residuetyes.dat.
Then added to .rtp file:
[ FVAL ]
[ atoms ]
CN C 0.357 0
ON O -0.5
Dear gromacs user,
Thank you for your previous reply. i am doing
Energy minimization using Steepest Descent method . When i do that i got the
following error
r
Steepest Descents converged to machine precision in 35 steps,
but did not reach the requested Fmax < 4
Uh-huh.. :-) ;-)
I visualized the .pdb in VMD and it seems OK.
All right, I will do the exercise for tonight. :-)
Thanks Mark.
Sincerely,
Shima
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Sunday, July 29, 2012 6:54 AM
On 29/07/2012 7:55 PM, Shima Arasteh wrote:
I listened to you absolutely and didn't proceed any other way! What I created
in .rtp file for FVAL ( like what you described sometime ago), is as below:
First of all added the FVAL to residuetyes.dat.
Then added to .rtp file:
[ FVAL ]
[ atoms ]
On 29/07/2012 8:08 PM, vidhya sankar wrote:
Dear gromacs user,
Thank you for your previous reply. i am doing
Energy minimization using Steepest Descent method . When i do that i got the
following error
r
Steepest Descents converged to machine precision in 35
There are several ways, usually I do like the following:
1. first construct one leaflet. Use "editconf -translate" to construct a small
box containing with 3 POPE 1 POPE
2. Use "genconf -nbox" to replicate the above in x,y dimension to get 64 lipids
3. Use "editconf -rotate -translate" to get th
Thanks dear Mark.
I don't use ignh. This is the command of pdb2gmx which I enter:
pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter
grompp does not give me the warning of that the atom names in the topology and
the coordinate file don't match, instead it gives me that there are no default
On 7/29/12 3:30 AM, James Starlight wrote:
Dear Gromacs Users!
I want to analyze protein-ligand polar interactions by means of g_hbond utility
In particular I want to obtain some map wich include information
aabout dynamics of the h bonds occurence between defined polar groups
of the protein
grompp warns me for some bonds and dihedrals ( no default ).
Ignoring such warnings gives me the same error as before ( some interactions
seems to be assigned multiple times)
Maybe I didn't modify the .rtp file correctly!
Sincerely,
Shima
- Original Message -
From: Shima Arasteh
To:
On 29/07/2012 9:31 PM, Shima Arasteh wrote:
grompp warns me for some bonds and dihedrals ( no default ).
Ignoring such warnings gives me the same error as before ( some interactions
seems to be assigned multiple times)
Maybe I didn't modify the .rtp file correctly!
Shrug... if you won't copy
Pleas don't shrug!
Sorry :-(
I attach the top file generated by pdb2gmx and this is what I see in terminal:
Processing chain 1 (177 atoms, 24 residues)
Identified residue FVAL1 as a starting terminus.
Identified residue GLY24 as a ending terminus.
8 out of 8 lines of specbond.dat converted succe
Pleas don't shrug!
Sorry :-(
I attach the top file generated by pdb2gmx and this is what I see in terminal:
Processing chain 1 (177 atoms, 24 residues)
Identified residue FVAL1 as a starting terminus.
Identified residue GLY24 as a ending terminus.
8 out of 8 lines of specbond.dat converted succ
Dear Mr Li
Thank you for your help!
Can you tell me more detials for the first step, for example, entire command
line?
thank you!
Best regards!
--- 12年7月29日，周日, Jianguo Li 写道：
> 发件人: Jianguo Li
> 主题: Re: [gmx-users] how to build a mixed lipid bilayer?
> 收件人: "Discussion list for
On 29/07/2012 10:17 PM, Shima Arasteh wrote:
Pleas don't shrug!
Sorry :-(
I attach the top file generated by pdb2gmx and this is what I see in terminal:
Processing chain 1 (177 atoms, 24 residues)
Identified residue FVAL1 as a starting terminus.
Identified residue GLY24 as a ending terminus.
8
So as I got the atomtypes have problem!
OK, I will do some exercise with charmm36 and acetyl.
Anyway, thanks for all your suggestions. However now my dead is going dizzy :)
Sincerely,
Shima
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Sunday
I did the exercise as you said.
A .pdb file of ACE and VAL. I ran the pdb2gmx, entered none as the N-terminus
and COO- as the C-terminus. The atomtyps that charmm selects for the acetyl is
as below:
1 CT3 1 ACE CH3 1 -0.27 12.011 ; qtot -0.27
2 HA
Dear Justin Thank you for your previous reply
When i run the .pdb2gmx_d -f 1OG2O.pdb -o 1OG2O.gro -p 1OG2O.top -renum
It runs successfully. But i have on issue. My PDB contains HIS residues in
both chain A and B I have selected
GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
The .rtp f
Dear All,
In my initial protein pdb structure I have added some external ligand
molecules and as a result of that there are several short contacts.
So, well, I minimized the system and then got the 'prot_min.gro' file.
Now after the equilibration run, I plotted the RMSD of the resulting
trajectory
see its not a big issue. Look at the atom types of the particular
RESIDUE in the pdb file and also have a look into the atom types
present in the rtp file. Now if these are matching properly then you
can choose any convenient name for that particular residue in the rtp
file. But the name of the par
On 2012-07-28 11:28, yousef nademi wrote:
hi gromacs users and especially Dr. Justine
in using the g_sgangle i have to define index file contain multiple of two
defining all the P and N atoms but after executing the g_sgangle i get the
message:something wrong with contents of index file
after d
On 7/29/12 9:39 AM, vidhya sankar wrote:
Dear Justin Thank you for your previous reply
When i run the .pdb2gmx_d -f 1OG2O.pdb -o 1OG2O.gro -p 1OG2O.top -renum
It runs successfully. But i have on issue. My PDB contains HIS residues in
both chain A and B I have selected
GROMOS96 53a6 force
On 30/07/2012 8:49 AM, Justin Lemkul wrote:
On 7/29/12 9:39 AM, vidhya sankar wrote:
Dear Justin Thank you for your previous reply
When i run the .pdb2gmx_d -f 1OG2O.pdb -o 1OG2O.gro -p 1OG2O.top
-renum
It runs successfully. But i have on issue. My PDB contains HIS
residues in both chai
On 29/07/2012 11:40 PM, Shima Arasteh wrote:
I did the exercise as you said.
A .pdb file of ACE and VAL. I ran the pdb2gmx, entered none as the N-terminus
and COO- as the C-terminus. The atomtyps that charmm selects for the acetyl is
as below:
1CT3 1ACECH3 1 -
On 30/07/2012 3:39 AM, tarak karmakar wrote:
Dear All,
In my initial protein pdb structure I have added some external ligand
molecules and as a result of that there are several short contacts.
So, well, I minimized the system and then got the 'prot_min.gro' file.
Now after the equilibration run,
Dear Gromacs users,
I tried to use "g_msd -s topol.tpr -f traj.xtc -o msd.xvg -trestart
500" to calculate the mean-squared displacements. But the results are
clearly erroneous: the first 2500 entries in the output are all
"-nan", and after that values stat constant (including zeros). I
suspected t
Dear Mark,
Thanks for the reply.
But one thing I am just wondering is that while calculating the RMSD,
I'm considering the backbone only. So I can take the initial pdb file
as reference for the trajectory. While doing so I see the RMSD graph
is continuing to increase and not getting equilibrium v
On 30/07/2012 4:49 PM, tarak karmakar wrote:
Dear Mark,
Thanks for the reply.
But one thing I am just wondering is that while calculating the RMSD,
I'm considering the backbone only. So I can take the initial pdb file
as reference for the trajectory. While doing so I see the RMSD graph
is conti
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