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meisam valizadeh kiamahalleh wrote:
Dear Justin
Good day to you
I would like to create a topology file of SWCNT with cisplatin inside
it. I also
have added the below 2 lines in atomname2type.n2t file;
C opls_240 0 12.011 3 C 0.142 C 0.142 C 0.142
C opls_239 0 12.011 2 C 0.142 C 0.142
And also added some bond parameters to ffbonded.itp file as below;
; Added by TEM for CNTs
[ 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
My commands and my error are;
editconf -f CNT_final.pdb -o CNT_final.gro -d 2.0
g_x2top -f CNT_final.gro -o CNT_final.top
.
.
.
Can not find forcefield for atom CL1_-1459 with 0 bonds
Can not find forcefield for atom PT2_-1460 with 0 bonds
Can not find forcefield for atom CL3_-1461 with 0 bonds
Can not find forcefield for atom _N4_-1462 with 0 bonds
Can not find forcefield for atom _N5_-1463 with 0 bonds
Can not find forcefield for atom _H6_-1464 with 0 bonds
Can not find forcefield for atom _H7_-1465 with 0 bonds
Can not find forcefield for atom _H8_-1466 with 0 bonds
Can not find forcefield for atom _H9_-1467 with 0 bonds
Can not find forcefield for atom _H10-1468 with 0 bonds
Can not find forcefield for atom _H11-1469 with 0 bonds
-------------------------------------------------------
Program g_x2top, VERSION 4.5.4
Source code file: g_x2top.c, line: 206
Fatal error:
Could only find a forcefield type for 0 out of 1469 atoms
Kindly, would you please help me to solve this problem? Should I need to
add
some bond parameters for Cisplatin as well? Does oplsaa forcefield can
support
cisplatin inside carbon nanotube?
First, since you have two separate molecules, the better approach is to create
two separate topologies, rather than trying to create a single one for two
different molecules. This will allow you greater flexibility later.
I do not know why g_x2top cannot find any correct force field parameters, since
the entries for the C atoms of the CNT appear reasonable. Likely the starting
geometry is poor and bonds cannot be found within +/- 10% of the 0.142 nm
reference distance, or the atoms are named strangely, but I'm just guessing
since you didn't post any of the screen output prior to what appears to be
cisplatin.
You certainly need to define parameters for cisplatin, but the bigger problem
there is that none of the force fields in Gromacs can deal with this species
without significant modification. Bonded and nonbonded terms will be missing
for nearly every interaction in this molecule, and none of the biomolecular
force fields in Gromacs readily deal with Pt. Developing quality parameters is
an advanced task that you should expect to take significant time (weeks to
months) unless you can find validated parameters elsewhere in the literature.
http://www.gromacs.org/Documentation/How-tos/Parameterization
-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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