On 2/13/20 8:56 AM, Atila Petrosian wrote:
Hi gromacs users,
I am doing MD simulation of my system (DPPC lipid + 2 drug molecules +
water molecules) using gromacs 2019.
I used ATB for drug molecules and Tieleman's web site for lipid molecules.
ATB uses a custom version of GROMOS96 that uses new atom types. You need
to use their force field files.
---------------------------------------
My topology file is as follows:
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#include "ffgmx.itp"
There is no reason to use this totally obsolete force field.
-Justin
#include "lipid.itp"
#include "dppc.itp"
#include "lig.itp"
#ifdef POSRES_LIG
#include "lig_posre.itp"
#endif
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
[ system ]
; name
dppc/lig/lig/sol
[ molecules ]
; Compound #mols
DPP 128
LIG 2
SOL 7173
---------------------------------------
My lig.itp file is as follows:
---------------------------------------
.
.
.
.
;
[ moleculetype ]
; Name nrexcl
LIG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 HC 1 LIG H27 1 0.131 1.0080
2 CAro 1 LIG C24 2 -0.130 12.0110
3 CAro 1 LIG C23 3 -0.130 12.0110
4 HC 1 LIG H26 4 0.131 1.0080
5 CAro 1 LIG C22 5 -0.119 12.0110
6 HC 1 LIG H25 6 0.135 1.0080
7 CAro 1 LIG C21 7 -0.039 12.0110
8 CAro 1 LIG C26 8 -0.119 12.0110
9 HC 1 LIG H29 9 0.135 1.0080
10 CAro 1 LIG C25 10 -0.130 12.0110
11 HC 1 LIG H28 11 0.131 1.0080
12 C 1 LIG C18 12 -0.051 12.0110
13 CH2 1 LIG C19 13 0.055 14.0270
14 CH3 1 LIG C20 14 0.020 15.0350
15 CAro 1 LIG C11 15 -0.025 12.0110
16 CAro 1 LIG C12 16 -0.040 12.0110
17 CAro 1 LIG C13 17 -0.117 12.0110
18 HC 1 LIG H15 18 0.137 1.0080
19 CAro 1 LIG C14 19 -0.133 12.0110
20 HC 1 LIG H16 20 0.131 1.0080
21 CAro 1 LIG C15 21 -0.129 12.0110
22 HC 1 LIG H17 22 0.131 1.0080
23 CAro 1 LIG C16 23 -0.133 12.0110
24 HC 1 LIG H18 24 0.131 1.0080
25 CAro 1 LIG C17 25 -0.117 12.0110
26 HC 1 LIG H19 26 0.137 1.0080
27 CAro 1 LIG C8 27 -0.076 12.0110
28 CAro 1 LIG C7 28 -0.079 12.0110
29 HC 1 LIG H12 29 0.139 1.0080
30 CAro 1 LIG C6 30 -0.184 12.0110
31 HC 1 LIG H11 31 0.143 1.0080
32 CAro 1 LIG C5 32 0.087 12.0110
33 CAro 1 LIG C10 33 -0.184 12.0110
34 HC 1 LIG H14 34 0.143 1.0080
35 CAro 1 LIG C9 35 -0.079 12.0110
36 HC 1 LIG H13 36 0.139 1.0080
37 OE 1 LIG O1 37 -0.219 15.9994
38 CH2 1 LIG C4 38 0.149 14.0270
39 CH2 1 LIG C3 39 0.101 14.0270
40 NTer 1 LIG N1 40 -0.267 14.0067
41 CH3 1 LIG C1 41 0.097 15.0350
42 CH3 1 LIG C2 42 0.097 15.0350
; total charge of the molecule: 0.000
[ bonds ]
; ai aj funct c0 c1
1 2 2 0.1090 1.2300e+07
2 3 2 0.1390 8.6600e+06
.
.
.
.
.
---------------------------------------
After using command: gmx solvate -cp final.gro -cs spc216.gro -p topol.top
-o system.gro, I encountered with the following error:
---------------------------------------
ERROR 1 [file lig.itp, line 65]:
Atomtype HC not found
---------------------------------------
How to resole it?
Best,
Atila
--
==================================================
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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