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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