GROMACS users
Cc:
Sent: Thursday, June 28, 2012 12:17 AM
Subject: Re: [gmx-users] Re: pdb2gmx error
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
[gmx-users] Re: pdb2gmx error
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
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
es in N-teminals) . Then I got regretful to remove it. Don't you
agree?
Sincerely,
Shima
- Original Message -
From: Justin A. Lemkul <jalemkul@>
To: Discussion list for GROMACS users <gmx-users@>
Cc:
Sent: Wednesday, June 27, 2012 10:25 PM
Subject: Re: [gmx-users] Re: pdb
sday, June 27, 2012 10:58 PM
Subject: Re: [gmx-users] Re: pdb2gmx error
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
2012 10:39 PM Subject: Re: [gmx-users] Re: pdb2gmx error
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 th
eliminate it? Honestly I'm a little confused here.
Sincerely,
Shima
- Original Message -
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Wednesday, June 27, 2012 10:39 PM
Subject: Re: [gmx-users] Re: pdb2gmx error
On 6/27/12 2:05 PM, Shima Arasteh
ely, Shima
- Original Message - From: Justin A. Lemkul To:
Discussion list for GROMACS users Cc: Sent:
Wednesday, June 27, 2012 10:25 PM Subject: Re: [gmx-users] Re: pdb2gmx error
On 6/27/12 1:52 PM, shounakb wrote:
Shima, I use gromacs-4.5.4. Without the FOR residue, my
gmx.ff/aminoacid
you agree?
Sincerely,
Shima
- Original Message -
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Wednesday, June 27, 2012 10:25 PM
Subject: Re: [gmx-users] Re: pdb2gmx error
On 6/27/12 1:52 PM, shounakb wrote:
> Shima, I use gromacs-4.5.4. Without the FO
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
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 1:52 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 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
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
ely,
Shima
- Original Message -
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Wednesday, June 27, 2012 9:55 PM
Subject: Re: [gmx-users] Re: pdb2gmx error
On 6/27/12 12:50 PM, Shima Arasteh wrote:
> OK.
> PDB FILE IS AS BELOW:
>
> HETATM 1 C
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
5 5.054 4.778
> ATOM 15 O SER 2 -5.272 4.628 4.966
>
>
> Sincerely,
> Shima
>
>
> - Original Message -
> From: Justin A. Lemkul <jalemkul@>
> To: Discussion list for GROMACS users <gmx-users@>
> Cc:
> Sent: Wednesda
- Original Message -
From: Justin A. Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Wednesday, June 27, 2012 9:14 PM
Subject: Re: [gmx-users] Re: pdb2gmx error
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
the first three residues in your .pdb file
so we can see what you're working with.
-Justin
Sincerely,
Shima
- Original Message -
From: Justin A. Lemkul
To: Shima Arasteh ; Discussion list for GROMACS users
Cc:
Sent: Wednesday, June 27, 2012 8:58 PM
Subject: Re: [gmx-users] Re
ma Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Wednesday, June 27, 2012 8:58 PM
Subject: Re: [gmx-users] Re: pdb2gmx error
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 a
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
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.
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