Hello everyone I’m trying to run a MD simulation in acetonitrile as solvent but when I execute gmx-solvate command, solvent molecules break apart making the number of atoms in .gro and .top files different from one another. Does anyone know how this issue can be addressed? I appreciate any help in advance.
- I have downloaded acetonitrile solvent box from virtualchemistry.org
- The force field I’m using is OPLS.
What exact command did you execute? did you update topology with this command?
This command can add solvent molecules, and along with this, it also updates topology file, so there is something you are fogetting.
I executed the command like this:
$ gmx solvate -cp system_box.gro -cs ACN.gro -p system.top -o system_solv.gro
Ayaz Anwar this is the topology file after this command is been executed:
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include AAC topology
#include "AAC.itp"
; Include ACN topology
#include "./oplsaa.ff/acetonitrile.itp" (in this part I have included .itp file for my solvent box)
; Include water topology
#include "./oplsaa.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 "./oplsaa.ff/ions.itp"
[ system ]
; Name
2 CRYSTAL FORMS OF LIPASE B FROM CANDIDA ANTARCTICA in water
[ molecules ]
; Compound #mols
Protein_chain_A 1
AAC 1
MOL 25650
this problem really shows itself in .gro file; for instance take a look at this part which is related to solvent molecules:
2MOL C 4645 0.023 2.949 0.315
3MOL H 4646 4.465 2.865 0.260
4MOL H 4647 0.008 3.033 0.247
5MOL H 4648 0.127 2.938 0.343
6MOL N 4649 4.397 3.001 0.545
7MOL H 4650 3.151 2.711 0.110
8MOL H 4651 3.187 2.748 0.284
9MOL H 4652 3.022 2.794 0.212
10MOL C 4653 3.189 2.900 0.159
11MOL N 4654 3.238 3.000 0.129
12MOL H 4655 0.437 0.110 3.527
13MOL H 4656 0.543 0.239 3.455
14MOL H 4657 0.482 0.264 3.621
15MOL C 4658 0.337 0.272 3.479
16MOL N 4659 0.238 0.316 3.442
17MOL H 4660 3.723 0.755 1.589
18MOL H 4661 3.823 0.618 1.670
19MOL H 4662 3.839 0.798 1.705
20MOL C 4663 3.918 0.713 1.527
21MOL N 4664 3.997 0.708 1.444
22MOL H 4665 1.525 3.138 1.967
23MOL H 4666 1.579 3.285 2.044
24MOL H 4667 1.460 3.285 1.903
25MOL C 4668 1.676 3.243 1.875
26MOL N 4669 1.776 3.243 1.818
27MOL H 4670 2.411 2.969 2.766
28MOL H 4671 2.347 2.984 2.612
29MOL N 4672 2.090 2.941 2.780
30MOL H 4673 2.495 3.484 2.474
31MOL H 4674 2.510 3.652 2.402
32MOL H 4675 2.372 3.542 2.361
33MOL C 4676 2.539 3.474 2.280
34MOL N 4677 2.588 3.415 2.194
35MOL H 4678 1.693 0.208 0.896
36MOL H 4679 1.737 0.110 0.752
37MOL H 4680 1.677 0.027 0.897
38MOL C 4681 1.865 0.103 0.921
39MOL N 4682 1.969 0.095 0.968
40MOL H 4683 1.040 2.408 1.236
41MOL H 4684 1.063 2.279 1.361
42MOL C 4685 1.038 2.195 1.180
43MOL N 4686 1.004 2.104 1.118
44MOL ML 4687 1.015 2.134 1.138 (this dummy atom which is actually the virtual site for CN triple bond is absent in some of the solvent molecules)
As per topology, you have
; Compound #mols
Protein_chain_A 1 >>> 1 protein mol
AAC 1 >>>> 1 AAC molecule, what is this?
MOL 25650 >>>> ~25,650 MOL molecules; is it acetonitrile (ACN)?
Since, you are using ACN as solvent, there is no need for water in topology.
My guess is that your ACN topology file is somehow not correct. ACN is Ch3-CN, but in this gro structure, it is something different. So check your ACN topology file. I tried to see it from the link you shared, but it was not working.
AAC is actually the ligand that I'm studying
ACN stands for acetonitrile
I must mention that the .itp file was included in virtualchemistry.org
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