Hi Sowmya,
This is an interesting simulation. Depending on what you're trying to get
out of the simulation, you may not need to add the HG atoms as dummy atoms.
If you define the cysteine residues you're changing as softcore, then it's
okay if they have a different number of atoms between region 1 and region
2.
On Fri, Feb 2, 2018 at 2:15 AM, Sowmya Indrakumar <soemya.kemi.dtu.dk>
wrote:
> Dear Amber users,
>
> I have run TI simulation on a system using pmemd (which needs single
> parmtop and inpcrd), I have in one state bonded disulphide bridge (state A)
> and in the other free cysteines (State B).
>
>
> As I understand, CYX is recognised as bonded and CYS as free cysteine in
> amber, hence the partial charges are adjusted accordingly. Since free
> cysteines have an extra atom (HG), should these be added as a dummy atom to
> the bonded cysteines??
>
>
> This is how I made the input files for running MD:
>
> 1) leap file
>
>
> source leaprc.protein.ff14SB
> source leaprc.water.tip3p
> loadAmberParams frcmod.ionsjc_tip3p
> m1 = loadpdb new_ss.pdb
> m2= loadpdb new.pdb
> bond m1.4.SG m1.30.SG
> bond m1.15.SG m1.37.SG
> bond m1.19.SG m1.39.SG
> bond m2.4.SG m2.30.SG
> bond m2.15.SG m2.37.SG
> protein = combine {m1 m2}
> set default nocenter on
> solvateoct protein TIP3PBOX 15.0
> savepdb protein protein_combine.pdb
> saveamberparm protein protein_sol.parm7 protein_sol.rst7
>
> quit
>
>
> 2) Timerge
>
> parmed protein_sol.parm7 <<_EOF
> loadRestrt protein_sol.rst7
> setOverwrite True
> tiMerge :1-40 :41-80 :19,39 :59,79
> outparm merged_protein.parm7 merged_protein.rst7
> quit
> _EOF
>
>
> 3)Minimisation using the merged_protein.parm7 merged_protein.rst7
>
> &cntrl
> imin = 1, ntmin = 2, maxcyc = 2000, ncyc=1000,
> ntpr = 20, ntwe = 20,
> dx0 = 1.0D-7,
> ntb = 1,
> iwrap = 1,
> icfe = 1, ifsc = 1, clambda = %L%, scalpha = 0.5, scbeta = 12.0,
> logdvdl = 0,
> timask1 = ':19,39',
> timask2 = ':41,42',
> scmask1 = ':19,39',
> scmask2 = ':41,42',
>
one possible issue here is you have residues 41 and 42 defined as softcore
for region 2, but in timerge you've specified scmask2 as residues 59 and
79. I haven't used timerge in a while so maybe I'm just not familiar, but
just make sure you've got the correct softcore masks.
>
> !method 2:
> !scmask1 = ':19,39', scmask2 = ':41,42',
> /
>
> &ewald
> /
>
> Looking forward to some comments on this.
> Thanks in advance
> Regards
> Sowmya
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Best,
Dan
--
Daniel J. Mermelstein, Ph.D candidate
McCammon & Walker Groups
Department of Chemistry & Biochemistry
University of California, San Diego
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 13 2018 - 22:30:02 PST
