[gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation
Justin Lemkul
jalemkul at vt.edu
Fri Oct 25 14:43:37 CEST 2019
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" <jalemkul at 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" <jordencabal at gmail.com
> <mailto:jordencabal at 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
>
> jalemkul at vt.edu <mailto:jalemkul at vt.edu> | (540) 231-3129
> http://www.thelemkullab.com <http://www.thelemkullab.com/>
>
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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
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
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