niaz poorgholami wrote:
Dear all
I am using Gromacs 4.5.3 to simulate a system including:
CNT+water+surfactant and I want to
use opls force field for my whole system.
so far I have done following things:
1.I copied oplsaa.ff folder in my working directory.
2.I added following lines to atomname2type.n2t
C opls_995 0 12.011 1 C 0.142
C opls_996 0 12.011 2 C 0.142 C 0.142
C opls_997 0 12.011 3 C 0.142 C 0.142 C 0.142
C opls_998 0 12.011 4 C 0.142 C 0.142 C 0.142 C 0.142
3.I added these to ffbonded.itp
[ bondtypes ]
C C 1 0.14210 478900
[ angletypes ]
C C C 1 120.000 397.480
[ dihedraltypes ]
C C 1 0.000 167.360 1
4.I added these to ffnonbonded.itp
opls_995 C 6 12.01100 0.000 A 3.851000e-01
4.39600e-01
opls_996 C 6 12.01100 0.000 A 3.851000e-01
4.39600e-01
opls_997 C 6 12.01100 0.000 A 3.851000e-01
4.39600e-01
opls_998 C 6 12.01100 0.000 A 3.851000e-01
4.39600e-01
5.I used g_x2top to create topology for CNT.
Command line was:
g_x2top -f cnt.pdb -o cnt.top -r cnt.rtp -name CNT -nexcl 5
6.I used TopolGen to produce the *.itp file for surfactant molecule.
7.I placed surfactant molecules around CNT.
8.I used editconf using this command:
editconf -f cnt_sur.pdb -o cnt_sur.gro -c -d 1 -bt cubic
9. I wrote a a .top file given below,
Include forcefield parameters
#include "./oplsaa.ff/forcefield.itp"
; Include topology for DTAB
#include "DTAB.itp"
; Include topology for CNT
#include "cnt.itp"
;
[ molecules ]
; molecule name nr.
DTAB 14
CNT 1
10.I called genbox with the command:
genbox -cp cnt_sur.gro -cs spc216.gro -p topol.top -o solv.gro
11.I added manually these to topol.top
; Include SPC water topology
#include "oplsaa.ff/spc.itp"
12. once I run grompp : grompp -f em.mdp -c solv.gro -p topol.top -o
ions.tpr
I got following errors:
Ignoring obsolete mdp entry 'title'
WARNING 1 [file ffbonded.itp, line 2704]:
Overriding Bond parameters.
old: 0.151 292880 0.151 292880
new: C C 1 0.14210 478900
So here grompp finds that you're overriding default force field parameters by
using some customized bond types. This may or may not be what you want/need, so
check carefully. If these are indeed what you are after, then there is no
problem here.
Generated 335790 of the 335790 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 335790 of the 335790 1-4 parameter combinations
ERROR 1 [file DTAB.itp, line 104]:
No default Bond types
To solve this error and the subsequent ones, check your topology at the quoted
line, identify which atom types the interaction pertains to, and determine which
parameters need to be added to ffbonded.itp. The "no default types" error comes
from the situation in which grompp cannot assign any parameters to the listed
interaction.
ERROR 2 [file DTAB.itp, line 105]:
No default Bond types
ERROR 3 [file DTAB.itp, line 241]:
No default Angle types
ERROR 4 [file DTAB.itp, line 242]:
No default Angle types
ERROR 5 [file DTAB.itp, line 244]:
No default Angle types
ERROR 6 [file DTAB.itp, line 245]:
No default Angle types
ERROR 7 [file DTAB.itp, line 249]:
No default Angle types
ERROR 8 [file DTAB.itp, line 302]:
No default Ryckaert-Bell. types
ERROR 9 [file DTAB.itp, line 303]:
No default Ryckaert-Bell. types
Excluding 3 bonded neighbours molecule type 'DTAB'
Excluding 5 bonded neighbours molecule type 'CNT'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file topol.top, line 27]:
System has non-zero total charge: 5.039999e+00
The fractional net charge here indicates that at least one of the topologies
(.itp) is broken such that you get a nonsensical sum of charges. It needs to be
an integer.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
