[gmx-users] grompp error for CNT+surfactant simulation

[Justin A. Lemkul]

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

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