[AMBER] Running gas phase TI with pmemd.CUDA.

From: Fanyu Zhao via AMBER <amber.ambermd.org>
Date: Mon, 5 Jun 2023 10:25:29 +0800

Dear amber users,

I'm trying to run TI in the gas phase. But it always gives me an error
message of "The CUDA code currently cannot handle TI with implicit solvent
models! Please use the serial code instead".

I was wondering if gas phase TI can only be performed with CPU and if I'm
correct with the process of creating a pdb file in gas phase.

Here's my input for a minimization.

Minimization with position restraint
  imin = 1, ntmin = 2, maxcyc = 10000,
  ntpr = 1000, ntwe = 1000,
  ntr = 1, restraint_wt = 100.0,
  restraintmask = '!.H= ',
  ntb=0,igb=6, cut = 9999.0, ioutfm = 1,
  icfe = 1, ifsc = 1, logdvdl = 0,
  scmask1=':10 & !.CA,C,N,O',
  scmask2=':3 & !.CA,C,N,O',

And here's the tleap file I used to generate a gas phase pdb file.

source leaprc.protein.ff14SB

com=loadpdb 1tvb_aftermd.pdb
unbound=loadpdb peptide.pdb

savepdb com wild_md_bound.pdb
saveamberparm com wild_md_bound.prmtop wild_md_bound.inpcrd

savepdb unbound wild_md_unbound.pdb
saveamberparm unbound wild_md_unbound.prmtop wild_md_unbound.inpcrd

Thank you so much!

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Received on Sun Jun 04 2023 - 19:30:02 PDT
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