Thank you very much!
I removed a few amino acid types from the cpin file and I do not get the
error anymore!
Maya
On Tue, Apr 17, 2018 at 10:49 AM, Cruzeiro,Vinicius Wilian D <
vwcruzeiro.ufl.edu> wrote:
> Hello Maya,
>
>
> Yes, there is a limit in the total number of residues. If you want, you
> may alter the following block at $AMBERHOME/src/pmemd/src/constantph.F90
> and recompile pmemd.
>
>
> ! Limits on the sizes of the data structures
> #define MAX_TITR_RES 50
> #define MAX_TITR_STATES 200
> #define MAX_ATOM_CHRG 1000
> #define MAX_H_COUNT 4
>
>
> However, it is advisable to reduce the number of residues in your cpin
> file rather than doing this. Increasing the number of residues reduces the
> computational efficiency of your simulation. In general, people only
> consider the residues of interest for titration at a given value of pH (or
> pH range) instead of titrating all possible residues. You may run a short
> simulation titrating all just to check which residues are important to you.
>
> I hope this helps,
> All the best,
>
>
> VinÃcius Wilian D Cruzeiro
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633
>
> ________________________________
> From: Maya Hauss <lordofthebhokaral.gmail.com>
> Sent: Tuesday, April 17, 2018 8:59:02 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Replica exchange in explicit solvent
>
> Dear Vincius,
>
> Thank you for your mail. You were right that I had not set the
> icnstph flag for the equilibriation. When I include that flag,
> the equilibriation fails with the same error as before.
>
> "forrtl: severe (18): too many values for NAMELIST variable"
>
> It must be something wrong with my cpin file, but I cannot
> figure out what that might be. I did create a new cpin for the
> explicit simulations. I have been trying to titrate HIP, CYS, LYS
> and TYR residues on my protein. So the equilibriation currently
> fails when I use the cpin generated using following command -
>
> cpinutil.py -p test.prmtop -resnames HIP LYS CYS TYR -igb 2 -o test.cpin
> -op test.mod.prmtop
>
> However, it runs successfully when I use the cpin from
>
> cpinutil.py -p test.prmtop -resnames HIP LYS CYS -igb 2 -o test.cpin -op
> test.mod.prmtop
>
> Is there a limit on the maximum number of residues that can be allowed to
> titrate? Could
> that be the reason for my error?
>
> Appreciate your help with this.
>
> Thank you
> Maya
>
>
>
>
> On Fri, Apr 13, 2018 at 3:36 PM, Cruzeiro,Vinicius Wilian D <
> vwcruzeiro.ufl.edu> wrote:
>
> > Hello Maya,
> >
> >
> > The cpin file will not be read unless icnstph=1 or 2, thus it was not
> read
> > during your equilibration. The cpin file for a implicit solvent
> simulation
> > is not going to be the same as for a explicit solvent simulation. Did you
> > use cpinutils.py to generate a new cpin for the explicit solvent
> > simulation? Just for testing, try to run a single simulation with
> icnstph=2
> > and without pH-REMD just to see it works.
> >
> >
> > Best,
> >
> >
> > VinÃcius Wilian D Cruzeiro
> >
> > PhD Candidate
> > Department of Chemistry, Physical Chemistry Division
> > University of Florida, United States
> >
> > Voice: +1(352)846-1633
> >
> > ________________________________
> > From: Maya Hauss <lordofthebhokaral.gmail.com>
> > Sent: Friday, April 13, 2018 3:23:12 PM
> > To: amber.ambermd.org
> > Subject: [AMBER] Replica exchange in explicit solvent
> >
> > Hi,
> >
> > I have been trying to combine the tutorials for ph replica exchange in
> > implicit solvent (https://urldefense.proofpoint.com/v2/url?u=http-
> > 3A__jswails.wikidot.com_ph-2Dremd&d=DwICAg&c=
> > pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-
> > DrdQBJXyFyocKAWXc&m=esjmUA8TbB6C6-FJ5Gm2efvFMjQdHImdZCKZOaUz1Pw&
> > s=t3Gkpr5qQeV7_VDSF0PD923Fo2KRjqs2rolAbwO5uAQ&e=), and constant ph
> > simulations in explicit solvent (https://urldefense.
> proofpoint.com/v2/url?u=https-3A__urldefense&d=DwIGaQ&c=
> pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-
> DrdQBJXyFyocKAWXc&m=bNv4yrBApZuh4XxAjNquC0YM9sF4rh0CmoqcbOU_xL8&s=
> tLM1nhl81jCpV9jqpKOAyyUBi9bnwwX850VifCNZArw&e=.
> > proofpoint.com/v2/url?u=http-3A__jswails.wikidot.com_&d=DwICAg&c=
> > pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-
> > DrdQBJXyFyocKAWXc&m=esjmUA8TbB6C6-FJ5Gm2efvFMjQdHImdZCKZOaUz1Pw&
> s=UccR2VU_
> > W3NDpX4pPiPHHJJZFOC2euDVE665NDel07s&e=
> > explicit-solvent-constant-ph-md) to perform replica exchange in explicit
> > solvent.
> >
> > I used the following input file for my production run
> >
> > imin=0, irest=1, ntx=5, ntxo = 2
> > ntpr=1000, ntwx=1000, nstlim=3000,
> > dt=0.002, ntt=3, tempi=300,
> > icnstph=2, ntcnstph=100, ntrelax=200,
> > solvph=8.0, saltcon=0.1, temp0=300.0,
> > ntc=2, ntf = 2, gamma_ln=1.0, ig=-1, ntp=1,
> > cut=8, ntb=2, iwrap=1, ioutfm=1,
> >
> > However, whenever i include the icnstph=2 parameter, I get the following
> > error
> > message *"forrtl: severe (18): too many values for NAMELIST variable" *
> > pointing
> > to the input cpin file. I did not have any problems using the same cpin
> > file
> > for the equilibriation run without the icnstph=2 parameter, or with the
> > entire imlicit solvent tutorial.I am not sure if I am doing something
> wrong
> > in combining the two tutorials. Would appreciate help with this issue. I
> am
> > using amber 16 update13.
> >
> > Maya
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
> > ambermd.org_mailman_listinfo_amber&d=DwICAg&c=
> > pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-
> > DrdQBJXyFyocKAWXc&m=esjmUA8TbB6C6-FJ5Gm2efvFMjQdHImdZCKZOaUz1Pw&
> > s=HuDG-Cq6vgq8pma6A9_VErLeaHB8n3yDdv8PAl5bW1Y&e=
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
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> ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=
> pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-
> DrdQBJXyFyocKAWXc&m=bNv4yrBApZuh4XxAjNquC0YM9sF4rh
> 0CmoqcbOU_xL8&s=GfarYP3-v_WgAaNC1_a8OjLpTmNw7W8m-_mjpM3ZMig&e=
> >
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Received on Wed Apr 18 2018 - 08:30:02 PDT
