Yes I made the changes on both.
Files I have attached here are files of two different systems(lig and
complex). They are generated at different system(one at PC and other at
cluster). cphstats command shows error with the file having more than 50
residue (if run at PC). However other with less than 50 works on both.
However I have modified code before compilation at cluster as well as on PC.
When I opened files on cygwin, there is only difference in spacing. I
thought may this was a reason.
Anyway I have performed analysis at cluster.
I works fine
Thanks for your reply and help
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On Mon, Mar 12, 2018 at 9:03 PM, Eric Lang <eric.lang.bristol.ac.uk> wrote:
> Hi Tasneem,
>
> Did you make the source code changes both on the cluster and on your PC?
> Because you need to, otherwise cphstats on your PC won't be able to parse a
> file with more than 50 ionisable residues coming from your cluster.
>
> Regarding the cpin files you sent, they do not have the same number of
> titrable residues: equil.cpin has 55 titrable residues, whereas
> lig.equil.cpin has only 36 residues with everything after GL4 203 being not
> in lig.equil.cpin.
>
> So there are definitely discrepancies there, either in the way you
> prepared the cpin files, or in the version of your code compiled on your
> cluster and on your PC.
>
> Hope this helps,
>
> Eric
>
>
>
> ________________________________
> From: Tasneem Kausar <tasneemkausar12.gmail.com>
> Sent: 12 March 2018 14:53
> To: AMBER Mailing List
> Subject: Re: [AMBER] Problem with cphstat
>
> Thank you for reply.
>
> Yes I have compiled amber after changing all those line.
>
> equil.cpin and md1.cpout files were generated at cluster. I was performing
> analysis at my PC. There is some change in the format of cpin file of my
> pc. May be this was the reason of error.
>
> cphstats runs properly at cluster.
>
> I am attaching here two files. First file is generated at cluster and
> second is at my PC (DELL- intel-i7).
>
>
>
>
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> On Mon, Mar 12, 2018 at 5:44 PM, Eric Lang <eric.lang.bristol.ac.uk>
> wrote:
>
> > Hi Tasneem,
> >
> >
> > Did you also change the following lines with your new values in some of
> > the files (for example in ./AmberTools/src/etc/calcpka.F90)?
> >
> >
> > integer, parameter :: STATEINF_FLD_C = 5
> >
> > integer, parameter :: TITR_RES_C = 50
> >
> > integer, parameter :: TITR_STATES_C = 200
> >
> > integer, parameter :: ATOM_CHRG_C = 1000
> >
> >
> > Did you recompile everything?
> >
> >
> > If you have done all of this, could you also add the equil.cpin so we
> can
> > have a look?
> >
> >
> > Cheers,
> >
> >
> > Eric
> >
> >
> >
> >
> > --
> >
> > Eric Lang
> >
> > BrisSynBio Postdoctoral Research Associate Modelling
> > Centre for Computational Chemistry
> > School of Chemistry - University of Bristol
> > Bristol BS8 1TS - United Kingdom
> >
> >
> > ________________________________
> > From: Tasneem Kausar <tasneemkausar12.gmail.com>
> > Sent: 12 March 2018 05:29
> > To: AMBER Mailing List
> > Subject: [AMBER] Problem with cphstat
> >
> > Dear all
> >
> > I have compiled the amber16 by modifying the following files
> > *./AmberTools/src/etc/calcpka.F90 *
> > *./AmberTools/src/pbsa/dynph.h *
> > *.**/AmberTools/src/cphstats/constants.h *
> > *./AmberTools/src/cphstats/parse_cpin.F90 *
> > *./AmberTools/src/gbnsr6/dynph.h *
> > *./AmberTools/src/sander/dynph.h *
> >
> > I have made these changes in the above files
> >
> > #define STATEINF_FLD_C 5
> > #define TITR_RES_C 200
> > #define TITR_STATES_C 800
> > #define ATOM_CHRG_C 4000
> > #define MAX_H_COUNT 4
> > #define FN_LEN 256
> >
> > I have performed CpH MD using amber16. There are 55 titerable residues in
> > the protein. The tool works fine while simulation. But during analysis it
> > gives error:
> >
> > cphstats -i equil.cpin pH_0/md1.cpout -o analysis/pH_0_calcpka.dat
> > --population analysis/pH_0_populations.dat
> > Error: Could not open or parse equil.cpin for reading!
> >
> > Is there any problem in code.
> > Please resolve the issue
> >
> >
> > Thanks in advance
> > _______________________________________________
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> > AMBER.ambermd.org
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> >
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Received on Mon Mar 12 2018 - 09:30:03 PDT
