Dear Prof. Case,
I have a mol2 file for CNT and frcmod. I am using gaff2 force field in
AMBER17. Yes, 1200 atoms consists of 1 whole residue (1 molecule of CNT).
CNT is fixed during the simulation
Here are the commands that I have used
tleap -s -f leaprc.protein.ff14SB
source leaprc.water.tip3p
source leaprc.gaff2
CNT=loadmol2 cnt.mol2
loadamberparams frcmod.cnt
savepdb CNT cnt.pdb
saveamberparm CNT input.prmtop input.inpcrd
solvatebox CNT TIP3PBOX 12
saveamberparm CNT solvated.prmtop solvated.inpcrd
savepdb CNT solvated.pdb
I can visualise input.prmtop and input.inpcrd (without water) in Chimera
whereas I cannot open solvated.prmtop and solvated.inpcrd in Chimera.
Chimera hangs while trying to open solvated.inpcrd and prmtop. Upon
visualization of solvated.pdb, I couldn't spot any issues with the file.
After minimisation, I run the solvated CNT system using below input script,
however the bonds of CNT appear distorted.
Relax water
LET WATER MOVE
&cntrl
timlim = 999999., nmropt = 0, imin = 0,
ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
ntpr = 500, ntwx = 500, ntwv = 0, ntwe = 0,
ntwr = 5000,
ntf = 2, ntb = 2,
cut = 10.0, nsnb = 20,
nstlim = 20000, nscm = 2500, iwrap = 1,
t = 0.0, dt = 0.002,
temp0 = 310.0, tempi = 310.0, tautp=0.5,
ntt = 1,
ntp =1 , taup = 1.0,
ntc = 2, tol = 0.00001,
ibelly=0, ntr=1,
restraintmask=":CNT" , restraint_wt=2.0,
&end
/
I also tried doing below steps to solvate using a different program
tleap -s -f leaprc.protein.ff14SB
source leaprc.water.tip3p
source leaprc.gaff2
CNT=loadmol2 cnt.mol2
loadamberparams frcmod.cnt
m1=loadpdb cnt-water.pdb
tleap will try to add atoms to the CNT (after 999) in the pdb file.
Your insight is appreciated.
Many thanks,
Neha
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On 11 September 2017 at 22:07, David A Case <david.case.rutgers.edu> wrote:
> On Mon, Sep 11, 2017, Neha Gandhi wrote:
> >
> > I have prepared frcmod file for carbon nanotube based on Hummer et al (
> > *Nature* *414*, 188-190 (8 November 2001). The CNT pdb file consists of >
> > 999 atoms (120 A long) and when I load it in tleap, tleap will not
> > recognise atoms beyond 999 and will try adding atoms again.
>
> 1. We would need to have the pdb file you used, and the commands you gave
> to tleap.
>
> Since Amber was written primarily for biomolecules, there could be many
> things
> "wrong" with a nanotube PDB file: too many atoms in a single residue,
> non-unique atom names, etc. Without more information, no one here can
> provide
> much help.
>
> >
> > I also tried using a single unit cell of carbon ring but then I faced
> > issues combining different unit cells together with a carbon-carbon bond.
>
> Same problem: just saying that you "faced issues" doesn't give anyone on
> the
> list much to go on.
>
> ....dac
>
>
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>
--
Regards,
Dr. Neha S. Gandhi,
Vice Chancellor's Research Fellow,
Queensland University of Technology,
2 George Street, Brisbane, QLD 4000
Australia
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Received on Mon Sep 11 2017 - 15:00:03 PDT
