Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Justin Lemkul]

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" :



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" 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

 --
 Gromacs Users mailing list


 * Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
 posting!

 * Can't post? Read
http://www.gromacs.org/Support/Mailing_Lists

 * For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Amit Jaiswal]

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 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 fcz1 1 1000 1000 1000#endif ; Include topology for ions#include "./charmm36-mar2019.ff/ions.itp"  [ system ]; NameProtein in water [ molecules ]; Compound #molsProtein_chain_A 1ZN 1NAD 1SOL 12908NA 4 Regards,Amit  23.10.2019, 20:41, "Justin Lemkul" :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 asa separate [moleculetype] in its own .itp file, the only valid atomnumber for position restraints is 1. Seehttp://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" : 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org>.  --==Justin A. Lemkul, Ph.D.Assistant ProfessorOffice: 301 Fralin HallLab: 303 Engel HallVirginia Tech Department of Biochemistry340 West Campus Dr.Blacksburg, VA 24061jalem...@vt.edu | (540) 231-3129http://www.thelemkullab.com== --Gromacs Users mailing list* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists* For (un)subscribe requests visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.   -- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Justin Lemkul]

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" :

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

--
Gromacs Users mailing list


* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
or send a mail to gmx-users-requ...@gromacs.org
.




--
==

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

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Jorden Cabal]

Dear Amit,
Yes, you need to correct the atom number in the "zn.itp" file in your case.
>From your co-ordinate file, it is clear that in order to restrain Zn atom
you need to put restraint potential on atom number corresponding to Zn atom
which is 4265 in your case instead of 2220. I think this should fix the
problem in your case. Try it and let me know if the problem persists.
Thank you.

On Tue, Oct 22, 2019 at 1:12 PM 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.
>
> 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" :
>
> 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
> --
> Gromacs Users mailing list
>
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Amit Jaiswal]

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. 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 3.136391THR HG23 4261 4.889 5.247 2.993391THR C 4262 4.600 5.071 3.244391THR OT1 4263 4.599 5.012 3.355391THR OT2 4264 4.496 5.082 3.173392ZN ZN 4265 7.278 6.612 5.838393NAD PA 4266 6.217 7.359 2.802393NAD O1A 4267 6.090 7.410 2.863393NAD O2A 4268 6.337 7.451 2.808393NAD O5B 4269 6.185 7.331 2.647393NAD C5B 4270 6.082 7.233 2.620   19.10.2019, 21:53, "Jorden Cabal" :Dear Amit,Your files look correct to me. If "2220" atom in your coordinate file isthe "Zn" atom, it should not be displaced because, from your mdp file andtopology setting you have restrained all the heavy atoms of Protein, Nadand Zn. I don't understand why it is happening. Even the restraining forceyou 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 selectedatom number for restraining. Also, if you are following the standardtutorial for energy minimization which do not restrain any atom, I suggestyou to check the position of Zn atom in structure you get after energyminimization. If the location of Zn ion is changed during the EM, then youwill need to minimize the system very carefully.Hope this will fix your issue.Thank you--Gromacs Users mailing list* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists* For (un)subscribe requests visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.   -- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Jorden Cabal]

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
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Amit Jaiswal]

Dear Jorden, Many thanks for your reply. I have mentioned the files below for you to have a look. Once again thanks for your time. NVT.mdp:title = Protein-ligand complex NVT equilibrationdefine = -DPOSRES -DPOSRES_LIG ; position restrain the protein and ligand; Run parametersintegrator = md ; leap-frog integratornsteps = 3 ; 2 * 5 = 100 psdt = 0.002 ; 2 fs; Output controlnstenergy = 500 ; save energies every 1.0 psnstlog = 500 ; update log file every 1.0 ps #includenstxout-compressed = 500 ; save coordinates every 1.0 ps; Bond parameterscontinuation = no ; first dynamics runconstraint_algorithm = lincs ; holonomic constraintsconstraints = h-bonds ; bonds to H are constrainedlincs_iter = 1 ; accuracy of LINCSlincs_order = 4 ; also related to accuracy; Neighbor searching and vdWcutoff-scheme = Verletns_type = grid ; search neighboring grid cellsnstlist = 20 ; largely irrelevant with Verletrlist = 1.2vdwtype = cutoffvdw-modifier = force-switchrvdw-switch = 1.0rvdw = 1.2 ; short-range van der Waals cutoff (in nm); Electrostaticscoulombtype = PME ; Particle Mesh Ewald for long-range electrostaticsrcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)pme_order = 4 ; cubic interpolationfourierspacing = 0.16 ; grid spacing for FFT; Temperature couplingtcoupl = V-rescale ; modified Berendsen thermostattc-grps = Protein_NAD Water_and_ions ; two coupling groups - more accuratetau_t = 0.1 0.1 ; time constant, in psref_t = 300 300 ; reference temperature, one for each group, in K; Pressure couplingpcoupl = no ; no pressure coupling in NVT; Periodic boundary conditionspbc = xyz ; 3-D PBC; Dispersion correction is not used for proteins with the C36 additive FFDispCorr = no; Velocity generationgen_vel = yes ; assign velocities from Maxwell distributiongen_temp = 300 ; temperature for Maxwell distributiongen_seed = -1 ; generate a random seed posre_zn.itp:; position restraints for ZN of Gromacs Runs One Microsecond At Cannonball Speeds [ position_restraints ]; i funct fcx fcy fcz2220 1 1000 1000 1000 posre_nad.itp:; position restraints for System_H* of GRowing Old MAkes el Chrono Sweat [ position_restraints ]; i funct fcx fcy fcz1 1 1000 1000 10002 1 1000 1000 10003 1 1000 1000 10004 1 1000 1000 10005 1 1000 1000 10006 1 1000 1000 10007 1 1000 1000 10008 1 1000 1000 10009 1 1000 1000 100010 1 1000 1000 100011 1 1000 1000 100012 1 1000 1000 100013 1 1000 1000 100014 1 1000 1000 100015 1 1000 1000 100016 1 1000 1000 100017 1 1000 1000 100018 1 1000 1000 100019 1 1000 1000 100020 1 1000 1000 100021 1 1000 1000 100022 1 1000 1000 100023 1 1000 1000 100024 1 1000 1000 100025 1 1000 1000 100026 1 1000 1000 100027 1 1000 1000 100028 1 1000 1000 100029 1 1000 1000 100030 1 1000 1000 100031 1 1000 1000 100032 1 1000 1000 100033 1 1000 1000 100034 1 1000 1000 100035 1 1000 1000 100036 1 1000 1000 100037 1 1000 1000 100038 1 1000 1000 100039 1 1000 1000 100040 1 1000 1000 100041 1 1000 1000 100042 1 1000 1000 100043 1 1000 1000 100044 1 1000 1000 100045 1 1000 1000 100046 1 1000 1000 100047 1 1000 1000 100048 1 1000 1000 100049 1 1000 1000 100050 1 1000 1000 100051 1 1000 1000 100052 1 1000 1000 100053 1 1000 1000 100054 1 1000 1000 100055 1 1000 1000 100056 1 1000 1000 100057 1 1000 1000 100058 1 1000 1000 100059 1 1000 1000 100060 1 1000 1000 100061 1 1000 1000 100062 1 1000 1000 100063 1 1000 1000 100064 1 1000 1000 100065 1 1000 1000 100066 1 1000 1000 100067 1 1000 1000 100068 1 1000 1000 100069 1 1000 1000 100070 1 1000 1000 1000   Regards,Amit  15.10.2019, 09:54, "Jorden Cabal" :Dear Amit,During equilibration you add positional restraint for protein, notice thatyou have added positional restraint for Zn ion, nad and protein. It shouldnot happen if you have taken the default values while generating thepositional restraints in gromacs. However I would like to look to your"nvt.mdp", "posre_zn.itp" and "posre_nad.itp" files, in order to commenton it.Thank youOn Sat, Oct 12, 2019 at 1:50 PM Amit Jaiswal  wrote:  Dear Jorden, Many thanks for your suggestions. I solved the index file problem as I created two groups namely Protein_Zn_NAD and the other being Na_Water. But when i ran NVT equilibration, the Zn ion again got displaced far away from its original position. I cannot figure out how can i constrain the Zn ion? I guess something is wrong in the topology file. I have included the last few lines of my topology file. Please have a look whenever you are free and correct me if something is mistakenly wrong. Thanks for your time and help. *; Include Position restraint file* *#ifdef POSRES* *#include "posre.itp"* *#endif* *; Include Position restraint file* *#ifdef POSRES* *#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 

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Justin Lemkul]

On 10/14/19 11:54 PM, ISHRAT JAHAN wrote:

Go through at the following link. Hope it will resolve the issue-
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html


Please update your bookmarks. That site is wildly outdated and will be 
taken offline soon.


Use the tutorial at http://www.mdtutorials.com/gmx/complex/index.html 
instead.


-Justin


On Tue, Oct 15, 2019 at 7:26 AM Jorden Cabal  wrote:


Dear Amit,
During equilibration you add positional restraint for protein, notice that
you have added positional restraint for Zn ion, nad and protein. It should
not happen if you have taken the default values while generating the
positional restraints in gromacs. However I would like to look to your
"nvt.mdp",  "posre_zn.itp" and "posre_nad.itp" files, in order to comment
on it.

Thank you

On Sat, Oct 12, 2019 at 1:50 PM Amit Jaiswal  wrote:


Dear  Jorden,

Many thanks for your suggestions. I solved the index file problem as I
created two groups namely Protein_Zn_NAD and the other being Na_Water.

But

when i ran NVT equilibration, the Zn ion again got displaced far away

from

its original position. I cannot figure out how can i constrain the Zn

ion?

I guess something is wrong in the topology file. I have included the last
few lines of my topology file. Please have a look whenever you are free

and

correct me if something is mistakenly wrong. Thanks for your time and

help.


*; Include Position restraint file*
*#ifdef POSRES*
*#include "posre.itp"*
*#endif*

*; Include Position restraint file*
*#ifdef POSRES*
*#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*

With kind regards,
Amit

11.10.2019, 18:10, "Jorden Cabal" :

Dear Amit,
Please check if the Zn ion is included in both the groups declared for
temperature coupling. If you notice that it is is included, you can

simply

create a group of all the atoms which is not in "Protein_NAD" group. You
can do this by using "!group_number" as far as I remember. Then try this,
it should work. Please mail if the problem persists.
Thank you and all the best.
--
Gromacs Users mailing list


* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.




--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.

--
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.





--
==

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

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[ISHRAT JAHAN]

Go through at the following link. Hope it will resolve the issue-
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/06_equil.html

On Tue, Oct 15, 2019 at 7:26 AM Jorden Cabal  wrote:

> Dear Amit,
> During equilibration you add positional restraint for protein, notice that
> you have added positional restraint for Zn ion, nad and protein. It should
> not happen if you have taken the default values while generating the
> positional restraints in gromacs. However I would like to look to your
> "nvt.mdp",  "posre_zn.itp" and "posre_nad.itp" files, in order to comment
> on it.
>
> Thank you
>
> On Sat, Oct 12, 2019 at 1:50 PM Amit Jaiswal  wrote:
>
> > Dear  Jorden,
> >
> > Many thanks for your suggestions. I solved the index file problem as I
> > created two groups namely Protein_Zn_NAD and the other being Na_Water.
> But
> > when i ran NVT equilibration, the Zn ion again got displaced far away
> from
> > its original position. I cannot figure out how can i constrain the Zn
> ion?
> > I guess something is wrong in the topology file. I have included the last
> > few lines of my topology file. Please have a look whenever you are free
> and
> > correct me if something is mistakenly wrong. Thanks for your time and
> help.
> >
> >
> > *; Include Position restraint file*
> > *#ifdef POSRES*
> > *#include "posre.itp"*
> > *#endif*
> >
> > *; Include Position restraint file*
> > *#ifdef POSRES*
> > *#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*
> >
> > With kind regards,
> > Amit
> >
> > 11.10.2019, 18:10, "Jorden Cabal" :
> >
> > Dear Amit,
> > Please check if the Zn ion is included in both the groups declared for
> > temperature coupling. If you notice that it is is included, you can
> simply
> > create a group of all the atoms which is not in "Protein_NAD" group. You
> > can do this by using "!group_number" as far as I remember. Then try this,
> > it should work. Please mail if the problem persists.
> > Thank you and all the best.
> > --
> > Gromacs Users mailing list
> >
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> >
> >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>


-- 
Ishrat Jahan
Research Scholar
Department Of Chemistry
A.M.U Aligarh
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Jorden Cabal]

Dear Amit,
During equilibration you add positional restraint for protein, notice that
you have added positional restraint for Zn ion, nad and protein. It should
not happen if you have taken the default values while generating the
positional restraints in gromacs. However I would like to look to your
"nvt.mdp",  "posre_zn.itp" and "posre_nad.itp" files, in order to comment
on it.

Thank you

On Sat, Oct 12, 2019 at 1:50 PM Amit Jaiswal  wrote:

> Dear  Jorden,
>
> Many thanks for your suggestions. I solved the index file problem as I
> created two groups namely Protein_Zn_NAD and the other being Na_Water. But
> when i ran NVT equilibration, the Zn ion again got displaced far away from
> its original position. I cannot figure out how can i constrain the Zn ion?
> I guess something is wrong in the topology file. I have included the last
> few lines of my topology file. Please have a look whenever you are free and
> correct me if something is mistakenly wrong. Thanks for your time and help.
>
>
> *; Include Position restraint file*
> *#ifdef POSRES*
> *#include "posre.itp"*
> *#endif*
>
> *; Include Position restraint file*
> *#ifdef POSRES*
> *#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*
>
> With kind regards,
> Amit
>
> 11.10.2019, 18:10, "Jorden Cabal" :
>
> Dear Amit,
> Please check if the Zn ion is included in both the groups declared for
> temperature coupling. If you notice that it is is included, you can simply
> create a group of all the atoms which is not in "Protein_NAD" group. You
> can do this by using "!group_number" as far as I remember. Then try this,
> it should work. Please mail if the problem persists.
> Thank you and all the best.
> --
> Gromacs Users mailing list
>
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
>
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Amit Jaiswal]

Dear  Jorden, Many thanks for your suggestions. I solved the index file problem as I created two groups namely Protein_Zn_NAD and the other being Na_Water. But when i ran NVT equilibration, the Zn ion again got displaced far away from its original position. I cannot figure out how can i constrain the Zn ion? I guess something is wrong in the topology file. I have included the last few lines of my topology file. Please have a look whenever you are free and correct me if something is mistakenly wrong. Thanks for your time and help.  ; Include Position restraint file#ifdef POSRES#include "posre.itp"#endif ; Include Position restraint file#ifdef POSRES#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 fcz1 1 1000 1000 1000#endif ; Include topology for ions#include "./charmm36-mar2019.ff/ions.itp"  [ system ]; NameProtein in water [ molecules ]; Compound #molsProtein_chain_A 1ZN 1NAD 1SOL 12908NA 4 With kind regards,Amit 11.10.2019, 18:10, "Jorden Cabal" :Dear Amit,Please check if the Zn ion is included in both the groups declared fortemperature coupling. If you notice that it is is included, you can simplycreate a group of all the atoms which is not in "Protein_NAD" group. Youcan do this by using "!group_number" as far as I remember. Then try this,it should work. Please mail if the problem persists.Thank you and all the best.--Gromacs Users mailing list* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists* For (un)subscribe requests visithttps://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.   -- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Jorden Cabal]

Dear Amit,
Please check if the Zn ion is included in both the groups declared for
temperature coupling. If you notice that it is is included, you can simply
create a group of all the atoms which is not in "Protein_NAD" group. You
can do this by using "!group_number" as far as I remember. Then try this,
it should work. Please mail if the problem persists.
Thank you and all the best.
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Amit Jaiswal]

Hello Everyone, I have solved this problem. However,i would like to ask how can I make an index file for Temperature Coupling for Protein_Zn_Ligand? When i tried to make the index group for the Protein_Zn_Ligand and I got the following error. Is the nvt simulation correct if i don't add Zn to the Temperature Coupling? Program: gmx grompp, version 2019.1Source file: src/gromacs/gmxpreprocess/readir.cpp (line 2667) Fatal error:Atom 4265 in multiple T-Coupling groups (1 and 2) The nvt parameters are mentioned below: title = Protein-ligand complex NVT equilibrationdefine = -DPOSRES -DPOSRES_LIG ; position restrain the protein and ligand; Run parametersintegrator = md ; leap-frog integratornsteps = 3 ; 2 * 5 = 100 psdt = 0.002 ; 2 fs; Output controlnstenergy = 500 ; save energies every 1.0 psnstlog = 500 ; update log file every 1.0 ps #includenstxout-compressed = 500 ; save coordinates every 1.0 ps; Bond parameterscontinuation = no ; first dynamics runconstraint_algorithm = lincs ; holonomic constraintsconstraints = h-bonds ; bonds to H are constrainedlincs_iter = 1 ; accuracy of LINCSlincs_order = 4 ; also related to accuracy; Neighbor searching and vdWcutoff-scheme = Verletns_type = grid ; search neighboring grid cellsnstlist = 20 ; largely irrelevant with Verletrlist = 1.2vdwtype = cutoffvdw-modifier = force-switchrvdw-switch = 1.0rvdw = 1.2 ; short-range van der Waals cutoff (in nm); Electrostaticscoulombtype = PME ; Particle Mesh Ewald for long-range electrostaticsrcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)pme_order = 4 ; cubic interpolationfourierspacing = 0.16 ; grid spacing for FFT; Temperature couplingtcoupl = V-rescale ; modified Berendsen thermostattc-grps = Protein_NAD Water_and_ions ; two coupling groups - more accuratetau_t = 0.1 0.1 ; time constant, in psref_t = 300 300 ; reference temperature, one for each group, in K; Pressure couplingpcoupl = no ; no pressure coupling in NVT; Periodic boundary conditionspbc = xyz ; 3-D PBC; Dispersion correction is not used for proteins with the C36 additive FFDispCorr = no; Velocity generationgen_vel = yes ; assign velocities from Maxwell distributiongen_temp = 300 ; temperature for Maxwell distributiongen_seed = -1 ; generate a random seed Please let me know if i am doing something wrong. Thanks for your time. With kind regards,Amit 11.10.2019, 12:09, "Amit Jaiswal" :Dear Jorden, Thanks for reply. I followed your suggestions and i got an error as follows: Command line:  gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr Ignoring obsolete mdp entry 'title'Setting the LD random seed to 1403244422Generated 100032 of the 100128 non-bonded parameter combinationsGenerating 1-4 interactions: fudge = 1Generated 65937 of the 100128 1-4 parameter combinations ERROR 1 [file posre_zn.itp, line 5]:  Atom index (2220) in position_restraints out of bounds (1-1).  This probably means that you have inserted topology section  "position_restraints"  in a part belonging to a different molecule than you intended to.  In that case move the "position_restraints" section to the right molecule.  ---Program:    gmx grompp, version 2019.1Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1818) Fatal error:There was 1 error in input file(s)  I guess there is something wrong with my topology file but i am unable to figure it out.My topology file looks like this: ; Include Position restraint file#ifdef POSRES#include "posre.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 fcz1 1 1000 1000 1000#endif ; Include topology for ions#include "./charmm36-mar2019.ff/ions.itp"#ifdef POSRES#include "posre_zn.itp"#endif [ system ]; NameProtein in water [ molecules ]; Compound #molsProtein_chain_A 1ZN 1NAD 1SOL 12908NA 4 Would you please let me know my mistake. Thanks for your time. With kind regards,Amit  10.10.2019, 15:41, "Jorden Cabal" :> Hi Amit,> The metal ion needs to be treated very very carefully so as to maintain> their co-ordination state with the nearby atoms of protein.> To do this, one needs to generate the parameter separately for the complex> formed by the metal ion with the protein residues because due to presence> of metal ion in the vicinity, the residues nearby will have different> parameters than other proteins especially the charge distribution. One> method of incorporating this model is to model the metal ion as a> dummy-particle metal ion complex model where the dummy particles carry some> partial charge and the whole complex represent the co-ordination state of> that particular atom.> I would suggest you to go through this paper> https://pubs.acs.org/doi/pdf/10.1021/jp501737x>> In case, you do not 

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Amit Jaiswal]

Dear Jorden, Thanks for reply. I followed your suggestions and i got an error as follows: Command line:  gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr Ignoring obsolete mdp entry 'title'Setting the LD random seed to 1403244422Generated 100032 of the 100128 non-bonded parameter combinationsGenerating 1-4 interactions: fudge = 1Generated 65937 of the 100128 1-4 parameter combinations ERROR 1 [file posre_zn.itp, line 5]:  Atom index (2220) in position_restraints out of bounds (1-1).  This probably means that you have inserted topology section  "position_restraints"  in a part belonging to a different molecule than you intended to.  In that case move the "position_restraints" section to the right molecule.  ---Program:    gmx grompp, version 2019.1Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1818) Fatal error:There was 1 error in input file(s)  I guess there is something wrong with my topology file but i am unable to figure it out.My topology file looks like this: ; Include Position restraint file#ifdef POSRES#include "posre.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 fcz1 1 1000 1000 1000#endif ; Include topology for ions#include "./charmm36-mar2019.ff/ions.itp"#ifdef POSRES#include "posre_zn.itp"#endif [ system ]; NameProtein in water [ molecules ]; Compound #molsProtein_chain_A 1ZN 1NAD 1SOL 12908NA 4 Would you please let me know my mistake. Thanks for your time. With kind regards,Amit  10.10.2019, 15:41, "Jorden Cabal" :> Hi Amit,> The metal ion needs to be treated very very carefully so as to maintain> their co-ordination state with the nearby atoms of protein.> To do this, one needs to generate the parameter separately for the complex> formed by the metal ion with the protein residues because due to presence> of metal ion in the vicinity, the residues nearby will have different> parameters than other proteins especially the charge distribution. One> method of incorporating this model is to model the metal ion as a> dummy-particle metal ion complex model where the dummy particles carry some> partial charge and the whole complex represent the co-ordination state of> that particular atom.> I would suggest you to go through this paper> https://pubs.acs.org/doi/pdf/10.1021/jp501737x>> In case, you do not want to go in that much detailed modeling of metal ion> for your system, which I think is very important to study metalloproteins,> another very simple method of solving the problem you are facing is to> treat metal ions as single sphere as you are treating in your system. To> avoid its displacement from its location, you need to apply some distance> restraints which is very easy to apply in Gromacs.> You can create the distance restraint using "*genrestr*" command. Please> note that applying any kind of restraint will definitely add some bias to> your simulation.> Thank you>> On Thu, Oct 10, 2019 at 1:05 PM Amit Jaiswal  wrote:>>>  Hello Everyone,  Would you please let me know what should we do when the zinc ion gets>>  displaced during simulation of a Protein-Zn-Ligand complex? What are the>>  possible options one can perform under such conditions? If possible, please>>  mention the steps needed to be performed briefly as i am new to GROMACS.>>  Your suggestions will help me a lot and thanks in advance.  With kind regards,>>  Amit>>  -->>  Gromacs Users mailing list  * Please search the archive at>>  http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before>>  posting!  * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists  * For (un)subscribe requests visit>>  https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or>>  send a mail to gmx-users-requ...@gromacs.org.> --> Gromacs Users mailing list>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists>> * For (un)subscribe requests visit> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.   -- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Jorden Cabal]

Hi Amit,
The metal ion needs to be treated very very carefully so as to maintain
their co-ordination state with the nearby atoms of protein.
To do this, one needs to generate the parameter separately for the complex
formed by the metal ion with the protein residues because due to presence
of metal ion in the vicinity, the residues nearby will have different
parameters than other proteins especially the charge distribution. One
method of incorporating this model is to model the metal ion as a
dummy-particle metal ion complex model where the dummy particles carry some
partial charge and the whole complex represent the co-ordination state of
that particular atom.
I would suggest you to go through this paper
https://pubs.acs.org/doi/pdf/10.1021/jp501737x

In case, you do not want to go in that much detailed modeling of metal ion
for your system, which I think is very important to study metalloproteins,
another very simple method of solving the problem you are facing is to
treat metal ions as single sphere as you are treating in your system. To
avoid its displacement from its location, you need to apply some distance
restraints which is very easy to apply in Gromacs.
You can create the distance restraint using "*genrestr*" command. Please
note that applying any kind of restraint will definitely add some bias to
your simulation.
Thank you

On Thu, Oct 10, 2019 at 1:05 PM Amit Jaiswal  wrote:

> Hello Everyone,
>
> Would you please let me know what should we do when the zinc ion gets
> displaced during simulation of a Protein-Zn-Ligand complex? What are the
> possible options one can perform under such conditions? If possible, please
> mention the steps needed to be performed briefly as i am new to GROMACS.
> Your suggestions will help me a lot and thanks in advance.
>
> With kind regards,
> Amit
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Reg: Zinc ion gets displaced during Protein-Zn-Ligand simulation

[Amit Jaiswal]

Hello Everyone,

Would you please let me know what should we do when the zinc ion gets displaced 
during simulation of a Protein-Zn-Ligand complex? What are the possible options 
one can perform under such conditions? If possible, please mention the steps 
needed to be performed briefly as i am new to GROMACS. Your suggestions will 
help me a lot and thanks in advance.

With kind regards,
Amit
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.