On 6/19/12 2:35 PM, Anik Sen wrote:
Hello Justin,
This is Anik again.
I checked the links. But could not understand fully. Am giving the part of the
topology file as given below, generated with the command
"pdb2gmx -f a.pdb -o b.pdb -p topol.top"
The topology file :
" 205 CL- 205 CL- Cl 205 -1 35.453 ; qtot 35
206 CL- 206 CL- Cl 206 -1 35.453 ; qtot 34
207 CL- 207 CL- Cl 207 -1 35.453 ; qtot 33
208 CL- 208 CL- Cl 208 -1 35.453 ; qtot 32
209 CL- 209 CL- Cl 209 -1 35.453 ; qtot 31
210 CL- 210 CL- Cl 210 -1 35.453 ; qtot 30
211 CL- 211 CL- Cl 211 -1 35.453 ; qtot 29
212 CL- 212 CL- Cl 212 -1 35.453 ; qtot 28
213 CL- 213 CL- Cl 213 -1 35.453 ; qtot 27
214 CL- 214 CL- Cl 214 -1 35.453 ; qtot 26
215 CL- 215 CL- Cl 215 -1 35.453 ; qtot 25
216 CL- 216 CL- Cl 216 -1 35.453 ; qtot 24
217 CL- 217 CL- Cl 217 -1 35.453 ; qtot 23
218 CL- 218 CL- Cl 218 -1 35.453 ; qtot 22
219 CL- 219 CL- Cl 219 -1 35.453 ; qtot 21
220 CL- 220 CL- Cl 220 -1 35.453 ; qtot 20
221 CL- 221 CL- Cl 221 -1 35.453 ; qtot 19
222 CL- 222 CL- Cl 222 -1 35.453 ; qtot 18
223 CL- 223 CL- Cl 223 -1 35.453 ; qtot 17
224 CL- 224 CL- Cl 224 -1 35.453 ; qtot 16
225 CL- 225 CL- Cl 225 -1 35.453 ; qtot 15
226 CL- 226 CL- Cl 226 -1 35.453 ; qtot 14
227 CL- 227 CL- Cl 227 -1 35.453 ; qtot 13
228 CL- 228 CL- Cl 228 -1 35.453 ; qtot 12
229 CL- 229 CL- Cl 229 -1 35.453 ; qtot 11
230 CL- 230 CL- Cl 230 -1 35.453 ; qtot 10
231 CL- 231 CL- Cl 231 -1 35.453 ; qtot 9
232 CL- 232 CL- Cl 232 -1 35.453 ; qtot 8
233 CL- 233 CL- Cl 233 -1 35.453 ; qtot 7
234 CL- 234 CL- Cl 234 -1 35.453 ; qtot 6
235 CL- 235 CL- Cl 235 -1 35.453 ; qtot 5
236 CL- 236 CL- Cl 236 -1 35.453 ; qtot 4
237 CL- 237 CL- Cl 237 -1 35.453 ; qtot 3
238 CL- 238 CL- Cl 238 -1 35.453 ; qtot 2
239 CL- 239 CL- Cl 239 -1 35.453 ; qtot 1
240 CL- 240 CL- Cl 240 -1 35.453 ; qtot 0
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "tip4p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif "
This includes the posre.itp as follows:
" ; In this topology include file, you will find position restraint
; entries for all the heavy atoms in your original pdb file.
; This means that all the protons which were added by pdb2gmx are
; not restrained.
[ position_restraints ]
; atom type fx fy fz
215 1 1000 1000 1000
216 1 1000 1000 1000
217 1 1000 1000 1000
218 1 1000 1000 1000
219 1 1000 1000 1000
220 1 1000 1000 1000
221 1 1000 1000 1000
222 1 1000 1000 1000
223 1 1000 1000 1000
224 1 1000 1000 1000
225 1 1000 1000 1000
226 1 1000 1000 1000
227 1 1000 1000 1000
228 1 1000 1000 1000
229 1 1000 1000 1000
230 1 1000 1000 1000
231 1 1000 1000 1000
232 1 1000 1000 1000
233 1 1000 1000 1000
234 1 1000 1000 1000
235 1 1000 1000 1000
236 1 1000 1000 1000
237 1 1000 1000 1000
238 1 1000 1000 1000
239 1 1000 1000 1000
240 1 1000 1000 1000 "
Now are these atoms already restrained, or we have to restrain tem by othr
means..
Provided that all of those atoms are in the same [moleculetype] in the topology,
this is a correct approach.
As after the minimisation step, the atoms are moving from their positions,
which i donot want.
Did you set the correct "define" statement in the .mdp file?
Also note that a position restraint does not completely prevent motion, it just
disfavors it. The magnitude of the energy penalty for displacement depends on
the force constant set in posre.itp. You can also use freezegrps to completely
immobilize any subset of atoms in the system.
-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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