leila separdar wrote:
I have installed gromacs version 4.5.3. when I want to use pdb2gmx for
generating .top and .gro files for 1000 argon atoms, in topology file I
have seen another atom O with mass 1.48594e-41 as below I do not know
what to do.I do not confront with such problems when I had 4.0.7 version
of gromacs. please help me. also I have used gromos43a1 force feild.
Sounds like it's related to (or the same as) a known issue:
http://redmine.gromacs.org/issues/618
Note that, for a monoatomic species (or any single molecule, really) pdb2gmx is
not necessary. Writing a simple "argon.itp" containing the one atom and its
nonbonded parameters is very trivial, since there aren't even any bonded
parameters to assign, just a single [atoms] directive. Then just #include it in
your .top.
-Justin
[ moleculetype ]
; Name nrexcl
Other_chain_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
; residue 1 GAS rtp GAS q 0.0
1 AR 1 GAS AR 1 0 1 ;
qtot 0
; residue 2 GAS rtp GAS q 0.0
2 O 2 GAS AR 2 0 1.48594e-41 ;
qtot 0
; residue 3 GAS rtp GAS q 0.0
3 O 3 GAS AR 3 0 1.48594e-41 ;
qtot 0
; residue 4 GAS rtp GAS q 0.0
4 O 4 GAS AR 4 0 1.48594e-41 ;
qtot 0
; residue 5 GAS rtp GAS q 0.0
5 O 5 GAS AR 5 0 1.48594e-41 ;
qtot 0
; residue 6 GAS rtp GAS q 0.0
6 O 6 GAS AR 6 0 1.48594e-41 ;
qtot 0
; residue 7 GAS rtp GAS q 0.0
--
========================================
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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