On 3/18/13 3:05 AM, Shima Arasteh wrote:
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. I checked again the itp files included
in my top file. They are matched correctly! Did I modified the settings incorrectly?
Clearly. Fatal errors mean something is very wrong. In principle, what you
showed before was correct. If that wasn't an actual topology snippet or you've
done something else wrong, then I haven't seen what it is.
-Justin
What would be other potent problems?
Please help me.
Thanks for your help.
Sincerely,
Shima
----- Original Message -----
From: Justin Lemkul <jalem...@vt.edu>
To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
Cc:
Sent: Sunday, March 17, 2013 5:19 PM
Subject: Re: Fwd: 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:
chainA_posre.itp and chainB_posre.itp
#genrestr -f system_solv_ions.gro -o chainA_posre.itp -fc 100000 100000 100000
-n index-chain.ndx
#genrestr -f system_solv_ions.gro -o chainB_posre.itp -fc 100000 100000 100000
-n index-chain.ndx
3.Next, I included the itp files as follow in my top file:
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef DPOSRE
#include "chainA_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef DPOSRE
#include "chainB_posre.itp"
#endif
4. I also added this line to my mdp file:
define = -DPOSRE
5. In addition I added these at the top of itp files for bothe restrained
chains:
#ifdef DPOSRE
#endif
Now when I run the command :
grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o minim.tpr
I don't get any errors.
But when I run the mdrun I don't see any position restraint terms in my log
file.
Would you please let me know your suggestions in this about? Did I do any steps
by mistake?
Yes, again there is a problem with the #ifdef statements. If you use:
#ifdef DPOSRE
...
#endif
the corresponding "define" statement is -DDPOSRE. Think of the first "D" in the
"define" statement as "I am defining the following string to be true." Your
.mdp file corresponds to the use of:
#ifdef POSRE
...
#endif
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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