Hai
Luckily, it worked. However, I do have some questions as well: When I have an elongated structure, and I wan to keep the molecule in that extension, I used the following restraint in my input files to restrain the molecule in a harmonic restraint but I am not sure if this is the right restraint as an internal one:
Minimize solvent(water)
&cntrl
imin=1,
maxcyc=10000, ncyc=5000,
ntb=1, ntp=0, cut=8.0
ntc=1, ntf=1,
ntr=0,restraintmask="!(:WAT)", restraint_wt=20.0
ntwx=50, ntpr=50, ntwr=50,
iwrap=1, ibelly=0, igb=0,
ioutfm=1, nmropt=1,
&end
/
&wt type='DUMPFREQ', istep1=10 /
&wt type='END' /
DISANG=dist_4840.RST
DUMPAVE=dist_4840_vs_t
LISTIN=POUT
LISTOUT=POUT
&rst
iat=2,382, r1=0, r2=80.024, r3=80.024, r4=999, rk2 = 1000.0, rk3 = 1000.0, /
and if correct, do we need to create one DUMPAVE file every single step by naming them differently, or we should rewrite on the first DUMPAVE file?
On the other hand, is there any means other than buffer option to control the size of the water box? namely, I have X number of water molecules to be added to the solute, is there any way to find the good estimate for the dimensions of the box?
Thanks
Ramin
________________________________
From: Hai Nguyen <nhai.qn.gmail.com>
Sent: Friday, March 31, 2017 4:37:45 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Issues Regaring the PDB files from Trajectory frames
Can you post exact error here?
cheers
Hai
On Fri, Mar 31, 2017 at 5:30 PM, Ramin Salimi <ramin.salimi01.utrgv.edu>
wrote:
> Hai
>
> That is right. I made that mistake but then corrected that but received
> similar errors of the same nature such that just the number of lines in the
> error changed.
>
>
> Ramin
>
> ________________________________
> From: Hai Nguyen <nhai.qn.gmail.com>
> Sent: Friday, March 31, 2017 4:27:14 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Issues Regaring the PDB files from Trajectory frames
>
> > At line 297 of file prmtop_dat.F90(unit=8, file= out_frame.pdb.4840)
>
> You're supposed to pass prmtop file, not pdb file (out_frame.pdb)?
>
> Hai
>
> On Fri, Mar 31, 2017 at 5:23 PM, Ramin Salimi <ramin.salimi01.utrgv.edu>
> wrote:
>
> > Dear Amber users
> >
> > I have picked some frames at different elongations from my trajectory
> file
> > to make PDB files. The following is my script to be used in cpptraj:
> >
> > parm revnelson.smd.prmtop
> > trajin smd.mdcrd
> > strip :WAT,Na+
> > center :1-24 mass origin
> > image origin center familiar
> > trajout out_frame.pdb pdb multi nobox onlyframes
> > 1412,1630,2790,3700,3933,4840,4958,5443,7278
> > Then, I solvate and neutralize them, and make topology and coordinate
> > files for each of the newly created pdb files. However, in the first
> > minimization step, I get the following:
> > At line 297 of file prmtop_dat.F90(unit=8, file= out_frame.pdb.4840)
> > Fortran runtime error= bad value during integer read OR
> > At line 71 of file rdparm.F90(unit=8, file= out_frame.pdb.4840)
> > Fortran runtime error= bad value during integer read OR
> >
> > At line 551 of file mdin_ctrl_dat.F90(unit=5, file=min1.in)
> >
> > Fortran runtime error= end of file
> > OR
> >
> > At line 587 of file mdread.F90((unit=5, file=min1.in)
> >
> > Fortran runtime error= end of file
> >
> > or similar errors.
> >
> > I think there is something wrong with my parameter and/or coordinate
> > file(s) created from the frame, but I do not know how to fix it.
> >
> > I have attached pdb file, the parameter and coordinate files from that
> pdb
> > file, AND ALSO, parameter(revnelson.smd.prmtop) and trajectory files
> from
> > which I extracted pdb files. The links to the attachments are provided
> > below:
> >
> > https://na01.safelinks.protection.outlook.com/?url=
> https%3A%2F%2F1drv.ms%2Fu%2Fs!AuyAusivBfCSiA3u1cQ9FZHpZrAl&
> data=02%7C01%7Cramin.salimi01%40utrgv.edu%7C32d3b81590c1427fe0d408d4787c
> b8ae%7C990436a687df491c91249afa91f88827%7C0%7C0%
> 7C636265924449752371&sdata=fBS5SAH8S0UielZ3wEkMYq%
> 2BTZEhZHmRiVdQZc4uBUpI%3D&reserved=0
> >
> > https://na01.safelinks.protection.outlook.com/?url=
> https%3A%2F%2F1drv.ms%2Fu%2Fs!AuyAusivBfCSiAiKNyix-6pS0fiC&
> data=02%7C01%7Cramin.salimi01%40utrgv.edu%7C32d3b81590c1427fe0d408d4787c
> b8ae%7C990436a687df491c91249afa91f88827%7C0%7C0%
> 7C636265924449752371&sdata=fhWBlkMOv9yNPAgImOOPGtd0jNOg0u
> hihjBkKd93Tio%3D&reserved=0<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fna01.safelinks&data=02%7C01%7Cramin.salimi01%40utrgv.edu%7Cc622dda4089c4cef110c08d4787e35b1%7C990436a687df491c91249afa91f88827%7C0%7C0%7C636265930837300492&sdata=0H9b%2BJO9sbuvb4TOS5bOZdzAOaQLuUOEwqBcsm5MM5Y%3D&reserved=0.
> protection.outlook.com/?url=https%3A%2F%2F1drv.ms%2Fu%2Fs%
> 25&data=02%7C01%7Cramin.salimi01%40utrgv.edu%
> 7C32d3b81590c1427fe0d408d4787cb8ae%7C990436a687df491c91249afa91f8
> 8827%7C0%7C0%7C636265924449752371&sdata=5UQBiPJQpFwc5uUKj3u1ek9%
> 2FHUEQU7ik9ED%2Ften0GqM%3D&reserved=0
> > 21AuyAusivBfCSiAiKNyix-6pS0fiC>
> >
> > Any help would be greatly appreciated.
> >
> > Thanks in Advance
> >
> > Ramin Salimi
> > _______________________________________________
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> 8827%7C0%7C0%7C636265924449752371&sdata=UjyWsWYNY6k3B6X%
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Received on Fri Mar 31 2017 - 16:30:03 PDT
