[AMBER] Small molecule break after minimization

From: Amen Shamim <amenshamim.gmail.com>
Date: Fri, 30 Aug 2019 22:16:46 +0900

Dear Amber group,

I have Si in my structure. I manually added bonds and angles in frcmod
file. Topology file generated without error. When I run Minimization
structure with ntc=2, structure is fine but without ntc Si making weird
bonding. In next step, in heating structure break in two parts at Si end.

Silicon angles and bonds are added from this site

>>antechamber -i THMP.pdb -fi pdb -o THMP.mol2 -fo mol2 -c bcc -nc 1
Welcome to antechamber 17.3: molecular input file processor.
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
   Status: pass
-- Check Unusual Elements --
Warning: Unusual element (Si) for atom (ID: 24, Name: Si).
GAFF does not have sufficient parameters for molecules having unusual
         elements (those other than H,C,N,O,S,P and halogens).
         To ensure antechamber works properly, one may need to designate
         bond types for bonds involved with unusual elements.
         To do so, simply freeze the bond types by appending "F" or "f"
         to the corresponding bond types in ac or mol2 files.
-- Check Open Valences --
   Status: pass
-- Check Geometry --
      for those bonded
      for those not bonded
   Status: pass
-- Check Weird Bonds --
   Status: pass
-- Check Number of Units --
   Status: pass
acdoctor mode has completed checking the input file.
Info: Total number of electrons: 112; net charge: 1
Running: /home/hpclab/Amen/amber16/bin/sqm -O -i sqm.in -o sqm.out

>>parmchk -i THMP.mol2 -f mol2 -o THMP.frcmod -a Y -w Y

Initial minimisation
imin=1, maxcyc=200, ncyc=50,
cut=16, ntb=0, igb=1,ntc=2,

Heating the minimised file
imin = 0, ntb = 1,
ntpr = 500, ntwx = 500,
ntt = 3, gamma_ln = 1.0,
temp0 = 300.0
nstlim = 100000, dt = 0.001,
cut = 8.0

frcmod file and pdb structure is attached with the email.
Can you closely look what parameters should I change?
Thank you

Best regards,

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Received on Fri Aug 30 2019 - 06:30:03 PDT
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