On 10/25/19 7:43 AM, Amit Jaiswal wrote:
Dear Jorden,
I tried the simulation by changing the residue number in .itp file but
it still goes out of the box during NVT. As Justin mentioned that the
naming of the residue is irrelevant, so I guess either I am doing some
minor mistake in
I had no issue with the name of the residue, I was pointing out that
there is only one valid atom *number* that can be in posre_zn.itp. It's
quite straightforward to apply the restraint (and fairly obvious when
it's wrong because grompp will throw a fatal error).
Are you sure that this "movement" of the ion is not simply a PBC effect?
Depending on your box shape, you may have to re-image very carefully.
-Justin
topology naming. So, I have included the order of topology file below.
Please Have a look and let me know if there is something wrong. I have
no idea why Zn ion is so hard to restrain. Thanks for your time.
*; Include Position restraint file*
*#ifdef POSRES*
*#include "posre.itp"*
*#endif*
*; Include ZN position restraints*
*#ifdef POSRES_ZN*
*#include "posre_zn.itp"*
*#endif*
*; Include ligand topology*
*#include "nad.itp"*
*; Ligand position restraints*
*#ifdef POSRES_LIG*
*#include "posre_nad.itp"*
*#endif*
*; Include water topology*
*#include "./charmm36-mar2019.ff/tip3p.itp"*
*#ifdef POSRES_WATER*
*; Position restraint for each water oxygen*
*[ position_restraints ]*
*; i funct fcx fcy fcz*
*1 1 1000 1000 1000*
*#endif*
*; Include topology for ions*
*#include "./charmm36-mar2019.ff/ions.itp"*
*[ system ]*
*; Name*
*Protein in water*
*[ molecules ]*
*; Compound #mols*
*Protein_chain_A 1*
*ZN 1*
*NAD 1*
*SOL 12908*
*NA 4*
Regards,
Amit
23.10.2019, 20:41, "Justin Lemkul" <jalem...@vt.edu>:
On 10/22/19 12:04 AM, Amit Jaiswal wrote:
Dear Jorden,
Thanks for your reply. As you have suggested, i found there is a
mismatch of the atom number in the zn.itp file and the .gro
file. I
have included few residues of .gro file for your convenience.
What i understand is that I have to rename the zn.itp file with
residue no. 4265 and not 2220. Please correct me if I am wrong.
The global atom number is irrelevant in defining position restraints
(and will actually trigger a warning in your case). If Zn is
defined as
a separate [moleculetype] in its own .itp file, the only valid atom
number for position restraints is 1. See
http://manual.gromacs.org/current/user-guide/run-time-errors.html#atom-index-n-in-position-restraints-out-of-bounds
-Justin
And also you suggested me to "minimize the system very
carefully".
What do you mean by this? Should i use lesser minimisation
steps ?
Thanks for your time and efforts.
With kind regards,
Amit
391THR HG22 4260 4.897 5.356 3.136
391THR HG23 4261 4.889 5.247 2.993
391THR C 4262 4.600 5.071 3.244
391THR OT1 4263 4.599 5.012 3.355
391THR OT2 4264 4.496 5.082 3.173
392ZN ZN 4265 7.278 6.612 5.838
393NAD PA 4266 6.217 7.359 2.802
393NAD O1A 4267 6.090 7.410 2.863
393NAD O2A 4268 6.337 7.451 2.808
393NAD O5B 4269 6.185 7.331 2.647
393NAD C5B 4270 6.082 7.233 2.620
19.10.2019, 21:53, "Jorden Cabal" <jordenca...@gmail.com
<mailto:jordenca...@gmail.com>>:
Dear Amit,
Your files look correct to me. If "2220" atom in your
coordinate
file is
the "Zn" atom, it should not be displaced because, from
your mdp
file and
topology setting you have restrained all the heavy atoms of
Protein, Nad
and Zn. I don't understand why it is happening. Even the
restraining force
you are taking is good enough.
I suggest you to check if the atom number 2220 in the
co-ordinate file
(.gro file) is Zn atom or not? If it is not then you have
wrongly
selected
atom number for restraining. Also, if you are following
the standard
tutorial for energy minimization which do not restrain
any atom, I
suggest
you to check the position of Zn atom in structure you get
after energy
minimization. If the location of Zn ion is changed during
the EM,
then you
will need to minimize the system very carefully.
Hope this will fix your issue.
Thank you
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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