# How to apply position constraint for a particular molecule? **URL:** \ **Category:** User discussions\ **Created:** [October 3, 2022, 6:25am UTC](https://gromacs.bioexcel.eu/t/how-to-apply-position-constraint-for-a-particular-molecule/4943 "2022-10-03T06:25:44Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![Shivangi](https://avatars.discourse-cdn.com/v4/letter/s/13edae/32.png) [@Shivangi](https://gromacs.bioexcel.eu/u/Shivangi)\ **Post date:** [October 3, 2022, 6:25am UTC](https://gromacs.bioexcel.eu/t/how-to-apply-position-constraint-for-a-particular-molecule/4943/1 "2022-10-03T06:25:44Z")
Hi everyone I am working on a problem containg few acid molecules at air water interface. I want to apply position restraint for acid during NVT/NPT equilibrium phase. So, I prepared the interface and placed the acid on its surface manually. To apply the position restraint i created the posre.itp file by using genresre command. when i am using grompp to equilibrate this system i am getting error as follows: Fatal error: Syntax error - File restr.itp, line 3 Last line read: ‘[position\_restraints]’ Invalid order for directive position\_restraints It seems that there is some problem in my itp file or in topology. I don’t know how to solve it. --------------------------------------------------------.top file--------------------------------------------------------------------- #include “oplsaa.ff/forcefield.itp” #ifdef POSRES #include “restr.itp” #endif #include “oplsaa.ff/tip3p.itp” [system] ; Name HNO3 in water [molecules] ; Compound #mols SOL 499 HNO3 1 ---------------------------------------------------------------posre.itp------------------------------------------------------------- ; position restraints for non-Water of 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984 [position\_restraints] ; i funct fcx fcy fcz 1498 1 1000 1000 1000 1499 1 1000 1000 1000 1500 1 1000 1000 1000 1501 1 1000 1000 1000 1502 1 1000 1000 1000 ~ This problem has bothered me for one week. Any suggestion would be of great help to me. Thanks a lot! ---
**Author:** ![nano](https://avatars.discourse-cdn.com/v4/letter/n/dec6dc/32.png) [@nano](https://gromacs.bioexcel.eu/u/nano)\ **Post date:** [October 3, 2022, 4:35pm UTC](https://gromacs.bioexcel.eu/t/how-to-apply-position-constraint-for-a-particular-molecule/4943/2 "2022-10-03T16:35:54Z")
You need to append the directive to your acid itp file (which seems not included). e.g., ```auto ; normal itp ....... [position_restraints] ; note the index 1 1 1000 1000 1000 2 1 1000 1000 1000 3 1 1000 1000 1000 4 1 1000 1000 1000 5 1 1000 1000 1000 ``` ---
**Author:** ![Shivangi](https://avatars.discourse-cdn.com/v4/letter/s/13edae/32.png) [@Shivangi](https://gromacs.bioexcel.eu/u/Shivangi)\ **Post date:** [October 4, 2022, 4:32am UTC](https://gromacs.bioexcel.eu/t/how-to-apply-position-constraint-for-a-particular-molecule/4943/3 "2022-10-04T04:32:13Z")
Hi nano, Thank for the message. As you pointed out, I added the directive to acid itp file but i am getting the error “ERROR 1 [file topo\_h.top, line 28]: Atom index (1) in position\_restraints out of bounds (1-0). This probably means that you have inserted topology section “position\_restraints” in a part belonging to a different molecule than you intended to.” i want to restraint the acid molecule. Here is my topology file #include “oplsaa.ff/forcefield.itp” [moleculetype] ; name nrexcl HNO3 3 [atoms] N opls\_966 0.968 1 O1 opls\_761 -0.408 1 O2 opls\_761 -0.497 1 O3 opls\_023 -0.526 1 H opls\_024 0.463 1 [bonds] N O1 N O2 N O3 O2 H [angles] O3 N O2 O1 N O2 O1 N O3 H O2 N [position\_restraints] ; note the index 1 1 1000 1000 1000 2 1 1000 1000 1000 3 1 1000 1000 1000 4 1 1000 1000 1000 5 1 1000 1000 1000 #include “oplsaa.ff/tip3p.itp” [system] ; Name HNO3 in water [molecules] ; Compound #mols SOL 499 HNO3 1 I tried checking it twice-thrice but couldn’t find error. Kindly help me to figure out what’s wrong in my topol.top file? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [October 4, 2022, 1:41pm UTC](https://gromacs.bioexcel.eu/t/how-to-apply-position-constraint-for-a-particular-molecule/4943/4 "2022-10-04T13:41:21Z")
> [@Shivangi](#): > > [moleculetype] > ; name nrexcl > HNO3 3 > > [atoms] > N opls\_966 0.968 1 > O1 opls\_761 -0.408 1 > O2 opls\_761 -0.497 1 > O3 opls\_023 -0.526 1 > H opls\_024 0.463 1 > > [bonds] > N O1 > N O2 > N O3 > O2 H > > [angles] > O3 N O2 > O1 N O2 > O1 N O3 > H O2 N This `[moleculetype]` definition is syntactically incorrect. It appears to be somewhat of a hybrid of `.rtp` and actual topology entry. Atoms need to be numbered, and all bonds, angles, etc. need to be specified by numbers, not atom names. You’re getting a fatal error because there are essentially zero atoms correctly defined, so you cannot apply restraints.