On 3/26/13 7:01 AM, Shima Arasteh wrote:
Hi Dear Justin
First of all, I request you that not to shout at me! I am so sorry to ask you
questions about position restraints again!
I haven't done any shouting, but statements like this seem to imply that I have.
The point of this forum is post your questions, so if things still aren't
clear, then you're welcome to post them. Hopefully I have never given anyone
the impression of anger or castigation in my answers. Sometimes I am terse, but
that's because I'm busy with my own work, and a short answer is preferable to a
long one.
I
know I have sent you such emails before, and you suggested me to read
include file mechanism in web site. I did this and also read some emails
in forum. But I think I have problems with include mechanism. Again I
got into the trouble about position restraining:
As you told me -DPOSRES will not trigger #ifdef POSRE or #ifdef DPOSRES.
I
have a system of POPC/ions/waters and a double chain protein inserted
in POPC bilayer. I put restraints on P headgroups and protein. I added
the define line to the mdp file as follow:
define = -DPOSRES_LIPID -DPOSRES
Then added the itp files to my top as follow:
; Include chain topologies
#include "topol_Protein_chain_A.itp"
#ifdef POSRE
#include "protein_chain_A_posre.itp"
#endif
#include "topol_Protein_chain_B.itp"
#ifdef POSRE
#include "protein_chain_B_posre.itp"
#endif
#ifdef POSRE requires -DPOSRE, not -DPOSRES as you have above. I've now said
that three times (and you said it above!), so please be mindful of the advice
you've been given and take care in what you're doing.
; Include POPC chain topology
#include "popc.itp"
#ifdef POSRES_LIPID
#include "lipid_posre.itp"
#endif
But when I run the grompp with -pp flag, I see that restraints on chain_B are
not included!
I don't see how that's possible. Position restraints for both chains are under
the control of the same #ifdef condition, as shown above. One cannot be
restrained without the other.
Then
I changed the numbering in protein_chain_B_posre.itp to what they are
in their original itp file, generated earlier by pdb2gmx. Do you agree
that it is the problem which I encountered with?
pdb2gmx should have provided you with suitable restraint .itp files when you
produced the original topology, and will have written suitable #ifdef blocks to
properly use them. Have you manipulated these files in some way? If you have,
start over. Use the files that pdb2gmx gave you until you can convince yourself
that you know how to use them correctly, then apply whatever custom restraints
you feel are necessary. Learn to walk before you run.
Now when I run grompp I see the restraints after each chains with the same
numbering.
I don't exactly know what this means. Are chains A and B identical? If they
are, then this makes sense.
-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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