All right. Thanks.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Wednesday, August 1, 2012 2:04 AM
Subject: Re: [gmx-users] Diagnosing + system blowing up
On 7/31/12 5:21 PM, Shima Arasteh wrote
You may get rid of the grompp warnings, but you also get rid of
reliability.
-Justin
Sincerely,
Shima
From: Shima Arasteh
To: Discussion list for GROMACS users
Sent: Tuesday, July 31, 2012 4:49 AM
Subject: Re: [gmx-users] Diagnosing + system blowing up
ers
Sent: Tuesday, July 31, 2012 4:49 AM
Subject: Re: [gmx-users] Diagnosing + system blowing up
I edited the grompp output and sent it to you. Bring that again here:
Generated 21528 of the 21528 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 18355 o
: Re: [gmx-users] Diagnosing + system blowing up
On 31/07/2012 7:16 AM, Shima Arasteh wrote:
> Wow! That was a fabulous explanation given to me. Thanks dear Mark! :-)
>
> I regenerated the topol.top to check the correctness of input and FF files.
> Some output has been changed howe
On 31/07/2012 7:16 AM, Shima Arasteh wrote:
Wow! That was a fabulous explanation given to me. Thanks dear Mark! :-)
I regenerated the topol.top to check the correctness of input and FF files.
Some output has been changed however a little bit. Now, I bring you all was
needed again:
1. rtp en
Wow! That was a fabulous explanation given to me. Thanks dear Mark! :-)
I regenerated the topol.top to check the correctness of input and FF files.
Some output has been changed however a little bit. Now, I bring you all was
needed again:
> 1. rtp entry
>
>[ FVAL ]
[ atoms ]
CN C 0.
On 30/07/2012 8:49 PM, Shima Arasteh wrote:
If you want further help, you will need to paste your .rtp entry(s), the
N-terminal fragment of your pdb2gmx -f input, pdb2gmx command line, full pdb2gmx
output, the N-terminal fragment of the grompp -c input, grompp >command line,
and full grom
>If you want further help, you will need to paste your .rtp entry(s), the
>N-terminal fragment of your pdb2gmx -f input, pdb2gmx command line, full
>pdb2gmx output, the N-terminal fragment of the grompp -c input, grompp
>>command line, and full grompp output. You may think your context is cl
On 30/07/2012 7:41 PM, Shima Arasteh wrote:
You are right, CT1 is incorrect for sure. But the other option is C(carbonyl
C) . Maybe I couldn't say it clearly.
The FVAL which I sent before through mailing list, is the result of this
formamide and the CGenff generation:
[ FVAL ]
[ atoms
CG1 HG13
>>
>> [ impropers ]
>> CN N ON H1
This is the new residue which I defined and sent you(as remember), I used these
parameters and atomtypes , and then went through mailing list and asked for
your help a few days ago.
All over , with this p
ima
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Monday, July 30, 2012 1:22 PM
Subject: Re: [gmx-users] Diagnosing + system blowing up
On 30/07/2012 6:36 PM, Shima Arasteh wrote:
Thanks dear Mark.
Actually the atomtype C is more suitable for C at
Ht
I found something similar to what I used here for my defined formyl group.Would
this be useful?
Sincerely,
Shima
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Monday, July 30, 2012 1:22 PM
Subject: Re: [gmx-users] Diagnosing + system blowi
On 30/07/2012 6:36 PM, Shima Arasteh wrote:
Thanks dear Mark.
Actually the atomtype C is more suitable for C atom of formyl and not CT1!
The same as before I get the no default bonds/angles/dihedral errors . You
explained what I am suppose.
I can understand the way of matching the coordinate fi
s
Cc:
Sent: Monday, July 30, 2012 6:29 AM
Subject: Re: [gmx-users] Diagnosing + system blowing up
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-termi
.
Mark
Sincerely,
Shima
- Original Message -
From: Shima Arasteh
To: Discussion list for GROMACS users
Cc:
Sent: Sunday, July 29, 2012 2:44 PM
Subject: Re: [gmx-users] Diagnosing + system blowing up
Uh-huh.. :-) ;-)
I visualized the .pdb in VMD and it seems OK.
All
... )
What do you suggest me? Any other homework to do? I will do!
Sincerely,
Shima
- Original Message -
From: Shima Arasteh
To: Discussion list for GROMACS users
Cc:
Sent: Sunday, July 29, 2012 2:44 PM
Subject: Re: [gmx-users] Diagnosing + system blowing up
Uh-huh
: Sunday, July 29, 2012 5:01 PM
Subject: Re: [gmx-users] Diagnosing + system blowing up
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
ussion list for GROMACS users
Sent: Sunday, July 29, 2012 4:07 PM
Subject: Re: [gmx-users] Diagnosing + system blowing up
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 interact
--
This is all I got.
I couldn't attach the .top file, it was too big.
Sincerely,
Shima
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Sunday, July 29, 2012 4:07 PM
Subject: Re: [gmx-users] Diagnosing + system blowing up
On 29/07/201
list for GROMACS users
Sent: Sunday, July 29, 2012 4:07 PM
Subject: Re: [gmx-users] Diagnosing + system blowing up
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
scussion list for GROMACS users
Cc:
Sent: Sunday, July 29, 2012 3:39 PM
Subject: Re: [gmx-users] Diagnosing + system blowing up
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
h
To: Discussion list for GROMACS users
Cc:
Sent: Sunday, July 29, 2012 3:39 PM
Subject: Re: [gmx-users] Diagnosing + system blowing up
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 n
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Sunday, July 29, 2012 2:48 PM
Subject: Re: [gmx-users] Diagnosing + system blowing up
On 29/07/2012 7:55 PM, Shima Arasteh wrote:
> I listened to you absolutely and didn't proceed any other way
day, July 29, 2012 1:14 AM
Subject: Re: [gmx-users] Diagnosing + system blowing up
On 7/28/12 2:47 PM, Shima Arasteh wrote:
Dear Mark, Thanks for your suggestions.
Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is
tha CA of the next resisue ( Valine), the bond 18-5 i
AM
Subject: Re: [gmx-users] Diagnosing + system blowing up
On 29/07/2012 4:47 AM, Shima Arasteh wrote:
>
>
> Dear Mark, Thanks for your suggestions.
> Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is
> tha CA of the next resisue ( Valine), the bond 18-5
t for GROMACS
users
Sent: Sunday, July 29, 2012 1:14 AM
Subject: Re: [gmx-users] Diagnosing + system blowing up
On 7/28/12 2:47 PM, Shima Arasteh wrote:
>
>
>
> Dear Mark, Thanks for your suggestions.
> Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5
On 29/07/2012 4:47 AM, Shima Arasteh wrote:
Dear Mark, Thanks for your suggestions.
Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is
tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all!
Uh-huh... there's a known initial issue with a bond bet
On 7/28/12 2:47 PM, Shima Arasteh wrote:
Dear Mark, Thanks for your suggestions.
Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is
tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all!
However I see this pair in the [pairs] section of topolo
Dear Mark, Thanks for your suggestions.
Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is
tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all!
However I see this pair in the [pairs] section of topology !
So I can get the result of an inappropri
Dear Mark, Thanks for your suggestions.
Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is
tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all!
However I see this pair in the [pairs] section of topology !
So I can get the result of an inappropria
It's a little bit challenging problem I've got into! Certainly for me!
Thanks for your suggestions.
Sincerely,
Shima
- Original Message -
From: Mark Abraham
To: Discussion list for GROMACS users
Cc:
Sent: Saturday, July 28, 2012 7:15 PM
Subject: Re: [gmx-users] Diagnoding + system
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