> Chimera hangs while trying to open solvated.inpcrd and prmtop.
That would be something to address with the Chimera authors.
Before you do, you may want to avoid having such a big residue.
> m1=loadpdb cnt-water.pdb
> tleap will try to add atoms to the CNT (after 999) in the pdb file.
I don't understand what you are doing. Best to copy/paste the tleap
session, minus the initialization phase.
Bill
On 9/11/17 2:38 PM, Neha Gandhi wrote:
> 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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Received on Mon Sep 11 2017 - 16:30:02 PDT
