[gmx-users] Re: Carbon Nanotubes with Cisplatin Inside it

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 8 14:07:04 CEST 2011


Please post all Gromacs-related correspondence to the gmx-users list.  I am not 
a private tutor.  I am CC'ing this message to the list as it may be of interest 
to others.  My comments are embedded below.

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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