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,
Vinícius 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,
>
>
> Vinícius 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
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Received on Tue Apr 17 2018 - 08:00:02 PDT
