n't matter at all, as long as you
> are consistent in invoking it.
>
> -Justin
>
>
>
>>
>> Sincerely,
>> Shima
>>
>>
>> __**__
>> From: Shima Arasteh
>> To: Justin Lemkul ; Discussion list for GROMACS us
nday, March 18, 2013 10:35 AM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I get the
fatal error. This error states that I have inserted topology section
"position_restraints" in a wrong place.
een what it is.
-Justin
What would be other potent problems?
Please help me.
Thanks for your help.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS users
Cc:
Sent: Sunday, March 17, 2013 5:19 PM
Subject: Re: Fwd: Fw:
users
Sent: Monday, March 18, 2013 10:35 AM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
To solve the problem, I changed all DPOSREs in if statments to POSRE. Again I
get the fatal error. This error states that I have inserted topology section
"position_restraints" in a
d: Fw: Fwd: [gmx-users] position restraints
On 3/17/13 6:50 AM, Shima Arasteh wrote:
> Thanks for your replies.
> As you suggested, I did as follows:
> 1. made index groups of two chains of my protein
> 2.Then applied genrestr in this command to generate 2 itp files:
On 3/17/13 6:50 AM, Shima Arasteh wrote:
Thanks for your replies.
As you suggested, I did as follows:
1. made index groups of two chains of my protein
2.Then applied genrestr in this command to generate 2 itp files:
chainA_posre.itp and chainB_posre.itp
#genrestr -f system_solv_ions.gro -o cha
by mistake?
Thanks in advance.
Sincerely,
Shima
From: Justin Lemkul
To: Discussion list for GROMACS users
Sent: Saturday, March 16, 2013 4:06 PM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/16/13 8:34 AM, Shima Arasteh wrote:
> Thanks.
> As I
On 3/16/13 8:34 AM, Shima Arasteh wrote:
Thanks.
As I understood from your emails, I need to make index groups of separate
chains of my protein, use the index file in order to use in genrestr command
and then include the specific itp files for each groups in top file?
Do you mean this? Am I r
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/16/13 7:09 AM, Shima Arasteh wrote:
> Do you mean that I need to make 2 backbone_posre.itp files for 2 chains?
> It would not be possible because I don't see any option for seperate chains
> when running genrestr c
On 3/16/13 7:09 AM, Shima Arasteh wrote:
Do you mean that I need to make 2 backbone_posre.itp files for 2 chains?
It would not be possible because I don't see any option for seperate chains
when running genrestr command.
You need to provide a sensible index group to genrestr to create such
asteh ; Discussion list for GROMACS
users
Sent: Saturday, March 16, 2013 2:21 PM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On Sat, Mar 16, 2013 at 9:40 AM, Shima Arasteh
wrote:
As you said I changed define in mdp file to define=-DPOSRE .
>
>I also included backbone.itp f
n/Errors
>
> Would you please give me suggestions?
>
The error message already did... Your chains are not identical. You are
applying the same position restraints file to them. GROMACS doesn't know
what you mean.
Mark
>
> Thanks in advance.
>
> Sincerely,
> Shima
>
please give me suggestions?
Thanks in advance.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Saturday, March 16, 2013 12:25 AM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/15/13 9:43 AM
please give me suggestions?
Thanks in advance.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Saturday, March 16, 2013 12:25 AM
Subject: Re: Fwd: Fw: Fwd: [gmx-users] position restraints
On 3/15/13 9:43 AM
On 3/15/13 9:43 AM, Shima Arasteh wrote:
I also included the position restraints as follows in my top file:
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRE
#include "backbone_posre.itp"
#include "strong_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef
I also included the position restraints as follows in my top file:
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRE
#include "backbone_posre.itp"
#include "strong_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef POSRE
#include "strong_posre.itp"
#include "b
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