I added the FOR residue as protein in residuetypes.dat file, but still says
it's not identified as protein/DNA/RNA.
Would you mind helping me with your suggestions?
Thanks in advance
Sincerely,
Shima
- Original Message -
From: Justin A. Lemkul
To: Discussion list for GROMACS users
As Justin suggested me, I added the FOR residue to the .rtp file of FF and then
added the FOR as a protein in residuetypes.dat . FOR is the first residue in
protein chain. I chose none as the N-terminus . But after processing the .pdb
file the FOR is identified itself but "not" identified as p
Dear Dmytro Kovalskyy,
The ARG CZ is at the end (tip of the ARG), what does the distances look like
over time? A floppy long amino acid? And your actual distance calculation?
Is it from a graphics/pdb file, or how is it measured?
Stephan
Original-Nachricht
> Datum: Tue, 26
Hi everybody,
I am going through the tutorial for membrane protein simulation which is
offered by gromacs.
I did everything just like it is described in the tutorial but when I want
to do the minimization in Step 3 after packing the lipids around the
protein I always get the error the
"number of co
On 6/27/12 1:23 AM, rama david wrote:
Hi Gromacs Friends,
I am doing Justin-lipid tutorialer
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
In these the npt.mdp has a parameter
refcoord_scaling = com
Why these parameter is introduced in NPT of lipid-prot
On 6/27/12 3:38 AM, Shima Arasteh wrote:
As Justin suggested me, I added the FOR residue to the .rtp file of FF and then added the
FOR as a protein in residuetypes.dat . FOR is the first residue in protein chain. I chose
none as the N-terminus . But after processing the .pdb file the FOR is
On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I am going through the tutorial for membrane protein simulation which is
offered by gromacs.
I did everything just like it is described in the tutorial but when I want
to do the minimization in Step 3 after pa
I added this line to the residuetypes.dat file:
FOR Protein
Then running this command:
pdb2gmx -f protein.pdb -water spc -ter
Written as blow:
Processing chain 1 (177 atoms, 25 residues)
Warning: Starting residue FOR0 in chain not identified as Protein/RNA/DNA.
Identified residue VAL1 as a s
Thank you Justin for your Explaination
Please Would you me the Reason Why these parameter is present in
Equilibration mdp and
not in production run mdp file ( for both lysozyme and lipid simulation )
With Best Wishes and regardsRama
--
gmx-users mailing listgmx-users@gromacs.org
http://
On 6/27/12 7:01 AM, rama david wrote:
Thank you Justin for your Explaination
Please Would you me the Reason Why these parameter is present in Equilibration
mdp and
not in production run mdp file ( for both lysozyme and lipid simulation )
It is only relevant when applying position restrain
Thank you Justin,
But you not added these parameter to the
Umbrella sampling NPT file.
Is any reason not to use these parameter in Umbrella sampling??
I run the simulation of peptide withought any
refcoord_scaling = com in mdp file
and now is it will affect result significantly??
Is it wrong
On 6/27/12 7:16 AM, rama david wrote:
Thank you Justin,
But you not added these parameter to the
Umbrella sampling NPT file.
Is any reason not to use these parameter in Umbrella sampling??
If it is missing, it's a simple typographical omission. I have adapted these
tutorials over many ye
On 6/27/12 6:38 AM, Shima Arasteh wrote:
I added this line to the residuetypes.dat file:
FOR Protein
Then running this command:
pdb2gmx -f protein.pdb -water spc -ter
Written as blow:
Processing chain 1 (177 atoms, 25 residues)
Warning: Starting residue FOR0 in chain not identified as Pr
Dear Gromacs Users,
I am using gromacs version 4.5.5. , while running grompp (for any
purpose i.e. minimization , equilibration etc. )
I am getting following screen output without any warning, error or
note relevant to it.
"Generated 830 of the 2346 non-bonded parameter combinations
Excluding 3 bo
On 6/27/12 7:36 AM, PAVAN PAYGHAN wrote:
Dear Gromacs Users,
I am using gromacs version 4.5.5. , while running grompp (for any
purpose i.e. minimization , equilibration etc. )
I am getting following screen output without any warning, error or
note relevant to it.
"Generated 830 of the 2346 non
Dear Gmx Users,
I obtained a protein-ligand complex from 100ns simulation. Now I am
pulling my ligand away from the protein after the energy minimzation
in water and equilibration of 100ps (two coupling baths: Protein,
LIG_Water_and_ions).
Then I proceed my pulling :
grompp -f pull.mdp -c npt.gro
On 27/06/12 05:20, Surya Prakash Tiwari wrote:
Dear Gromacs users,
I am having a very strange problem with "Nose Hoover thermostat with
Parrinello-Rahman barostat" NPT simulations for a system of an ion of
charge +2 in flexible water molecules. Flexible water is taken from J.
Chem. Phys. 124, 02
Hi Justin,
thank you for your answer. Now it worked and I could do the minimization.
But now I have the same problem again but now the difference is 630.
So what I did is that I ran the minimization and everything worked. And
than I used the
"perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink
Got it already.
Thank you!!
>
>
> On 6/27/12 4:31 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>> I am going through the tutorial for membrane protein simulation which is
>> offered by gromacs.
>> I did everything just like it is described in the tutorial but when I
>> w
On 6/27/12 7:48 AM, Steven Neumann wrote:
Dear Gmx Users,
I obtained a protein-ligand complex from 100ns simulation. Now I am
pulling my ligand away from the protein after the energy minimzation
in water and equilibration of 100ps (two coupling baths: Protein,
LIG_Water_and_ions).
Then I proce
On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul wrote:
>
>
> On 6/27/12 7:48 AM, Steven Neumann wrote:
>>
>> Dear Gmx Users,
>>
>> I obtained a protein-ligand complex from 100ns simulation. Now I am
>> pulling my ligand away from the protein after the energy minimzation
>> in water and equilibra
On 6/27/12 9:36 AM, Steven Neumann wrote:
On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul wrote:
On 6/27/12 7:48 AM, Steven Neumann wrote:
Dear Gmx Users,
I obtained a protein-ligand complex from 100ns simulation. Now I am
pulling my ligand away from the protein after the energy minimz
Anyway, thanks for your reply .
I appreciate you.
Sincerely,
Shima
Sincerely,
Shima
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Sent: Wednesday, June 27, 2012 3:54 PM
Subject: Re: [gmx-users] H-atoms in .hdb file
On 6/27/12 6:38 AM, Sh
Thank you Justin.
On Wed, Jun 27, 2012 at 2:39 PM, Justin A. Lemkul wrote:
>
>
> On 6/27/12 9:36 AM, Steven Neumann wrote:
>>
>> On Wed, Jun 27, 2012 at 1:51 PM, Justin A. Lemkul wrote:
>>>
>>>
>>>
>>> On 6/27/12 7:48 AM, Steven Neumann wrote:
Dear Gmx Users,
I obtained
Hi everybody,
I want to make an index with "make_ndx".
But when I just wanted to group SOL and CL and Protein and DPPC it
tells me when I want to run grompp afterwards that there are some residues
not indexed.
I thought that that might be because the NA-ions are not grouped. But when
I want
On 6/27/12 11:08 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to make an index with "make_ndx".
But when I just wanted to group SOL and CL and Protein and DPPC it
tells me when I want to run grompp afterwards that there are some residues
not indexed.
Cop
Hi all,
I got this error :
Atom CA is used in an interaction of type improper in the topology database,
but an atom of that name was not found in residue number 2.
I checked the pdb file and rtp file.
.rtp file:
[ SER ]
[ atoms ]
N N -0.280 0
H H 0.280 0
CA
Hi,
C and O should be atoms 14 and 15 (i.e. the last two atoms)
Hope this works!
Shima Arasteh wrote
>
> Hi all,
>
> I got this error :
> Atom CA is used in an interaction of type improper in the topology
> database, but an atom of that name was not found in residue number 2.
> I checked the
Hi,
C and O should go last (i.e. their atom numbers should be 14 and 15
respectively.
Hope this works!
Regards,
Shounak
Shima Arasteh wrote
>
> Hi all,
>
> I got this error :
> Atom CA is used in an interaction of type improper in the topology
> database, but an atom of that name was not fo
You mean the order of C and O should be changed in .pdb file? If yes, it didn't
work!
Sincerely,
Shima
- Original Message -
From: shounakb
To: gmx-users@gromacs.org
Cc:
Sent: Wednesday, June 27, 2012 8:39 PM
Subject: [gmx-users] Re: pdb2gmx error
Hi,
C and O should go last (i.e.
On 6/27/12 12:25 PM, Shima Arasteh wrote:
You mean the order of C and O should be changed in .pdb file? If yes, it didn't
work!
The order of atoms in the .pdb file is irrelevant. What may be the issue is
that when pdb2gmx is reporting the error, it is printing its own internal
residue nu
Hi,
i meant to perform a free energy calculation to get the chemical
potential of water, and made a number of input files based on the excellent
tutorial
by Justin Lemkul.
(Without thinking) I also tried using a tabulated potential for electrostatics
with: coulombtype = User
but it seems to wor
I know that no missing atom is here.
As the fatal error is about atom name CA, I checked it, but it's actually
existed in both .rtp and pdb in agreement.
Please help me, I don't know what to do :(
Sincerely,
Shima
- Original Message -
From: Justin A. Lemkul
To: Shima Arasteh ; Discus
On 6/27/12 12:43 PM, Shima Arasteh wrote:
I know that no missing atom is here.
As the fatal error is about atom name CA, I checked it, but it's actually
existed in both .rtp and pdb in agreement.
Please help me, I don't know what to do :(
Please copy and paste the entirety of the first thre
OK.
PDB FILE IS AS BELOW:
HETATM 1 C FOR 0 -0.721 1.600 1.249
HETATM 2 O FOR 0 -0.839 2.806 1.453
ATOM 3 N VAL 1 -1.227 0.728 2.125
ATOM 4 CA VAL 1 -1.918 1.159 3.323
ATOM 5 C VAL 1 -1.969 2.678
Hi,
removing the HETATMs worked for me when i used AMBER99SB's rtp file.
What force field are you using? Have you added the FOR topology manually (I
know this is besides the point about the problem with serine) AMBER99SB
seemed to only have topology for acetate [ACE]
I am also learning through t
If I remove HETATMs, then what about the FOR residue?
Thanks for your suggestions.
Sincerely,
Shima
- Original Message -
From: shounakb
To: gmx-users@gromacs.org
Cc:
Sent: Wednesday, June 27, 2012 9:42 PM
Subject: [gmx-users] Re: pdb2gmx error
Hi,
removing the HETATMs worked for
On 6/27/12 12:50 PM, Shima Arasteh wrote:
OK.
PDB FILE IS AS BELOW:
HETATM1 C FOR 0 -0.721 1.600 1.249
HETATM2 O FOR 0 -0.839 2.806 1.453
ATOM 3 N VAL 1 -1.227 0.728 2.125
ATOM 4 CA VAL 1 -1.918 1.159 3.323
ATOM
I know it's much better to use a non-deprecated ff. But what could I do? I
have to regenerate the results of simulation done by gmx.ff . Aren't there any
solution to pass this step?
I PROMISE YOU AND ME TO REPEAT THE SIMULATION WHIT A MODERN FF AS SOON AS
POSSIBLE :)
Sincerely,
Shima
---
On 6/27/12 1:35 PM, Shima Arasteh wrote:
I know it's much better to use a non-deprecated ff. But what could I do? I
have to regenerate the results of simulation done by gmx.ff . Aren't there any
solution to pass this step?
I have no idea how to make gmx.ff work. I "solved" the issue by co
Dear Justin,
Again, I appreciate you. I learn much from you, feeling happy :)
Thanks a lot.
Sincerely,
Shima
- Original Message -
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Wednesday, June 27, 2012 10:10 PM
Subject: Re: [gmx-users] Re: pdb2gmx error
O
Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp
file works fine for the sequence you originally specified. (pdb2gmx executes
without any errors)
I guess you added the FOR cap's topology yourself?
Justin, could this be an issue?
Sincerely,
Shounak
--
View this messag
On 6/27/12 1:52 PM, shounakb wrote:
Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp
file works fine for the sequence you originally specified. (pdb2gmx executes
without any errors)
I guess you added the FOR cap's topology yourself?
Justin, could this be an issue?
Dear Shounak,
So what's about the FOR residue? I can't eliminate it. I guess if I do as you
suggest, I need to add the FOR to n.tdb and then the procedure would be
different!
Yes, I added the FOR to rtp file on my own.
Sincerely,
Shima
- Original Message -
From: shounakb
To: gmx-use
On 6/27/12 1:58 PM, Shima Arasteh wrote:
Dear Shounak,
So what's about the FOR residue? I can't eliminate it. I guess if I do as you
suggest, I need to add the FOR to n.tdb and then the procedure would be
different!
You do not need to add FOR to a .tdb entry. These directives are only to m
:))
I can't eliminate it, I decided to do , but when I studied about the structure
of protein ( consists of 2 monomers, which form a dimer in lipid bilayer, and
the reason of this formation is the existence of formyl residues in N-teminals)
. Then I got regretful to remove it. Don't you agree?
On 6/27/12 2:05 PM, Shima Arasteh wrote:
:)) I can't eliminate it, I decided to do , but when I studied about the
structure of protein ( consists of 2 monomers, which form a dimer in lipid
bilayer, and the reason of this formation is the existence of formyl residues
in N-teminals) . Then I got
So as you said it doesn't matter to remove the FOR residue. But I can't
understand why the representation of FOR is still required!
And, you suggest me to use another forcefield to produce the topology and then
go on whit it by gmx ? Would I need to maintain the FOR in the new FF or
eliminate
On 6/27/12 2:23 PM, Shima Arasteh wrote:
So as you said it doesn't matter to remove the FOR residue. But I can't
understand why the representation of FOR is still required!
I did not say that. Your last message gave the reason why the formyl group is
necessary. Have I misunderstood? This
You are right.
OK, the reason of adding FOR is what I explained a few minutes ago.
All over, I'm supposed to use a modern FF . ( In similar researches I found
CHARMM is suitable, so I would add FOR as the procedure explained in
GROMACS.ORG)
For now, because I wanna regenerate an old simulatio
Hi Shima,
i do not think pdb2gmx uses the tdb files. However, I feel that the FOR
tdb entries should go to aminoacids.c.tdb and not aminoacids.n.tdb
I saw your other thread where you have described the FOR topology you added.
I think the atoms should be CA and O and their respective atom types
On 6/27/12 2:49 PM, shounakb wrote:
Hi Shima,
i do not think pdb2gmx uses the tdb files. However, I feel that the FOR
tdb entries should go to aminoacids.c.tdb and not aminoacids.n.tdb
Both of these assertions are incorrect. The *only* Gromacs program that uses
.tdb files is pdb2gmx.
On 6/27/12 2:42 PM, Shima Arasteh wrote:
You are right.
OK, the reason of adding FOR is what I explained a few minutes ago.
All over, I'm supposed to use a modern FF . ( In similar researches I found
CHARMM is suitable, so I would add FOR as the procedure explained in
GROMACS.ORG)
This so
Dear Gmx Users,
I am wondering whether would you advise to run NVT, NPT (position
restrained) and before the pulling simulation e.g of the ligand from
protein-ligand complex? As I saw in Justin tutorial he equilibrate the
system with only NPT ensemble before pulling. Is that really sufficent
e.g.
On 6/27/12 4:30 PM, Steven Neumann wrote:
Dear Gmx Users,
I am wondering whether would you advise to run NVT, NPT (position
restrained) and before the pulling simulation e.g of the ligand from
protein-ligand complex? As I saw in Justin tutorial he equilibrate the
system with only NPT ensemble
sorry about the previous post! I have not yet looked at the code for pdb2gmx
(and a lot of other stuff).
I think the formyl-valine idea is pretty cool and found this thread very
informative.
Thank you!
Shounak
Justin A. Lemkul wrote
>
> On 6/27/12 2:49 PM, shounakb wrote:
>> Hi Shima,
>> i
Dear Justin,
All right. I'll give it a try. Thanks Justin.
I hope it works and the FOR issue would be terminated
Sincerely,
Shima
- Original Message -
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Thursday, June 28, 2012 12:17 AM
Subject: Re: [gmx-use
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