/// https://www.charmmtutorial.org/index.php/Full_example
public static SPsfCrd Solvate
(IEnumerable <string> toplines
, IEnumerable <string> parlines
, IEnumerable <string> psflines_prot
, IEnumerable <string> crdlines_prot
, IEnumerable <string> crdlines_water
)
{
string tempbase = @"C:\temp\";
SPsfCrd psfcrd;
using (var temp = new HTempDirectory(tempbase, null))
{
temp.EnterTemp();
string topname = "top.rtf"; HFile.WriteAllLines(topname, toplines);
string parname = "par.prm"; HFile.WriteAllLines(parname, parlines);
string psfname_prot = "prot.psf"; HFile.WriteAllLines(psfname_prot, psflines_prot);
string crdname_prot = "prot.crd"; HFile.WriteAllLines(crdname_prot, crdlines_prot);
string crdname_water = "water.crd"; HFile.WriteAllLines(crdname_water, crdlines_water);
string psfname_protwater = "protwater.psf";
string crdname_protwater = "protwater.crd";
string conf_inp = @"* Run Segment Through CHARMM
*
! read topology and parameter files
read rtf card name $$topname$$
read para card name $$parname$$
! read the psf and coordinate file
read psf card name $$psfname_prot$$
read coor card name $$crdname_prot$$
! Read in water sequence
read sequence tip3 46656
! Generate new segment for the water
generate bwat noangle nodihedral
! Read the water PDB coordinates and append them to the protein
read coor card append name $$crdname_water$$
! Delete waters which overlap with protein
delete atom sort -
select .byres. (segid bwat .AND. type oh2 .and. -
((.not. (segid bwat .OR. hydrogen)) .around. 2.5)) end
! set headstr = rhdo with a crystal dimension of @greatervalue
set headstr = test xxx
! we want to do a quick-and-dirty minimization to remove bad contacts. Therefore, we should
! set up shake and the non-bond parameters again.
shake bonh param sele all end
nbond inbfrq -1 elec fswitch vdw vswitch cutnb 16. ctofnb 12. ctonnb 10.
mini sd nstep 100 nprint 1 tolgrd 100.0
! use Expanded I/O format
ioform extended
! since we've changed the structure by adding waters, we need to write out a new PSF
write psf card name $$psfname_protwater$$
* new_1cbn-18126-1-solv.psf
* solvation: @headstr
*
write coor card name $$crdname_protwater$$
* new_1cbn-18126-1-solv.crd
* solvation: @headstr
*
stop
".Replace("$$topname$$", topname)
.Replace("$$parname$$", parname)
.Replace("$$psfname_prot$$", psfname_prot)
.Replace("$$crdname_prot$$", crdname_prot)
.Replace("$$crdname_water$$", crdname_water)
.Replace("$$psfname_protwater$$", psfname_protwater)
.Replace("$$crdname_protwater$$", crdname_protwater)
;
HFile.WriteAllText("conf.inp", conf_inp);
System.Console.WriteLine("Run the following command at " + temp + " :");
System.Console.WriteLine(" $ charmm < conf.inp");
System.Console.WriteLine(" or $ mpd&");
System.Console.WriteLine(" $ mpirun -n 38 charmm_M < conf.inp");
System.Console.WriteLine("Then, copy " + psfname_protwater + " and " + crdname_protwater + " to " + temp);
while (true)
{
bool next = HConsole.ReadValue <bool>("Ready for next? ", false, null, false, true);
if (next)
{
if (HFile.ExistsAll(psfname_protwater, crdname_protwater))
{
string[] psflines_protwater = HFile.ReadAllLines(psfname_protwater);
string[] crdlines_protwater = HFile.ReadAllLines(crdname_protwater);
psfcrd = new SPsfCrd
{
psflines = psflines_protwater,
crdlines = crdlines_protwater,
};
break;
}
System.Console.WriteLine("DO, copy " + psfname_protwater + " and " + crdname_protwater + " to " + temp);
}
}
temp.QuitTemp();
}
return(psfcrd);
}
/// https://www.charmmtutorial.org/index.php/Full_example
public static string[] MinimizeCrd
(IEnumerable <string> toplines
, IEnumerable <string> parlines
, IEnumerable <string> psflines
, IEnumerable <string> crdlines
, string conf_inp_mini
)
{
string tempbase = @"C:\temp\";
if (conf_inp_mini == null)
{
conf_inp_mini = @"
mini sd nstep 100
mini abnr nstep 1000 nprint 10000 tolg 0.0001
! mini abnr nstep 1000 nprint 100 tolg 0.01
! mini abnr nstep 10000000 nprint 100 tolg 0.00
! mini abnr nstep 1000000 nprint 100 tolg 10.00 ! target-min-step1-tolg-10_00.crd
! mini abnr nstep 1000000 nprint 100 tolg 1.00 ! target-min-step2-tolg-1_00.crd
! mini abnr nstep 1000000 nprint 100 tolg 0.10
! mini sd nstep 10000 ! target-min-step3-sd10000.crd
! mini abnr nstep 1000000 nprint 100 tolg 0.01 ! target-min-step4-tolg-0_01.crd
! mini abnr nstep 10000 nprint 100 tolg 0.0001 ! target-min-step5-tolg-0_0001.crd
! mini abnr nstep 10000 nprint 100 tolg 0.000001 ! target-min-step6-tolg-0_000001.crd
! mini abnr nstep 10000 nprint 100 tolg 0.000000 ! target-min-step7-tolg-0_000000.crd
";
}
string[] mincrdlines;
using (var temp = new HTempDirectory(tempbase, null))
{
temp.EnterTemp();
string topname = "top.rtf"; HFile.WriteAllLines(topname, toplines);
string parname = "par.prm"; HFile.WriteAllLines(parname, parlines);
string psfname = "target.psf"; HFile.WriteAllLines(psfname, psflines);
string crdname = "target.crd"; HFile.WriteAllLines(crdname, crdlines);
string mincrdname = "target-minimized.crd";
string conf_inp = @"* Minimize PDB
*
! read topology and parameter file
read rtf card name $$topname$$
read param card name $$parname$$
! read the psf and coordinate file
read psf card name $$psfname$$
read coor card name $$crdname$$
! set up shake
shake bonh param sele all end
! set up electrostatics, since we're not using PME, set up switching
! electrostatics
nbond inbfrq -1 elec fswitch vdw vswitch cutnb 16. ctofnb 12. ctonnb 10.
energy
coor copy comp
" + conf_inp_mini + @"
coor rms
ioform extended
write coor card name $$mincrdname$$
* Initial minimization, no PME.
*
stop
";
conf_inp = conf_inp.Replace("$$topname$$", topname)
.Replace("$$parname$$", parname)
.Replace("$$psfname$$", psfname)
.Replace("$$crdname$$", crdname)
.Replace("$$mincrdname$$", mincrdname)
;
HFile.WriteAllText("conf.inp", conf_inp);
System.Console.WriteLine("Run the following command at " + temp + " :");
System.Console.WriteLine(" $ charmm < conf.inp");
System.Console.WriteLine(" or $ mpd&");
System.Console.WriteLine(" $ mpirun -n 38 charmm_M < conf.inp");
System.Console.WriteLine("Then, copy target-minimized.crd to " + temp);
while (true)
{
bool next = HConsole.ReadValue <bool>("Ready for next? ", false, null, false, true);
if (next)
{
if (HFile.ExistsAll(mincrdname))
{
mincrdlines = HFile.ReadAllLines(mincrdname);
break;
}
System.Console.WriteLine("DO, copy target.psf and target.crd to " + temp);
}
}
temp.QuitTemp();
}
return(mincrdlines);
}
/// https://www.charmmtutorial.org/index.php/Full_example
public static string[] Hessian
(IEnumerable <string> toplines
, IEnumerable <string> parlines
, IEnumerable <string> psflines
, IEnumerable <string> crdlines
)
{
string tempbase = @"C:\temp\";
string[] mincrdlines;
using (var temp = new HTempDirectory(tempbase, null))
{
temp.EnterTemp();
string topname = "top.rtf"; HFile.WriteAllLines(topname, toplines);
string parname = "par.prm"; HFile.WriteAllLines(parname, parlines);
string psfname = "target.psf"; HFile.WriteAllLines(psfname, psflines);
string crdname = "target.crd"; HFile.WriteAllLines(crdname, crdlines);
string mincrdname = "target-minimized.crd";
string conf_inp = @"* Minimize PDB
* Minimize PDB
*
! read topology and parameter file
read rtf card name top.rtf
read param card name par.prm
! read the psf and coordinate file
read psf card name target.psf
read coor card name target.crd
! set up shake
shake bonh param sele all end
! set up electrostatics, since we're not using PME, set up switching
! electrostatics
nbond inbfrq -1 elec fswitch vdw vswitch cutnb 16. ctofnb 12. ctonnb 10.
energy
coor copy comp
! mini sd nstep 100
! mini abnr nstep 1000 nprint 10000 tolg 0.0000
! ! mini abnr nstep 1000 nprint 100 tolg 0.01
! ! mini abnr nstep 10000000 nprint 100 tolg 0.00
! ! mini abnr nstep 1000000 nprint 100 tolg 10.00 ! target-min-step1-tolg-10_00.crd
! ! mini abnr nstep 1000000 nprint 100 tolg 1.00 ! target-min-step2-tolg-1_00.crd
! ! mini abnr nstep 1000000 nprint 100 tolg 0.10
! ! mini sd nstep 10000 ! target-min-step3-sd10000.crd
! ! mini abnr nstep 1000000 nprint 100 tolg 0.01 ! target-min-step4-tolg-0_01.crd
! ! mini abnr nstep 10000 nprint 100 tolg 0.0001 ! target-min-step5-tolg-0_0001.crd
! ! mini abnr nstep 10000 nprint 100 tolg 0.000001 ! target-min-step6-tolg-0_000001.crd
! ! mini abnr nstep 10000 nprint 100 tolg 0.000000 ! target-min-step7-tolg-0_000000.crd
!
!
! coor rms
!
! ioform extended
!
! write coor card name target-minimized.crd
! * Initial minimization, no PME.
! *
! VIBRAN NMOD 20 ATOM FSWITCH rdie eps 4.0 VDW VSHIFT cutnb 13.0 ctofnb 12.0 CTONNB 8.0
!
! DIMB ITERations 500 TOLErance 0.04 PARDim 200 IUNMode 21 DWIN
!
! WRITe SECOnd-derivatives card
! BOMLEV -2
! VIBRAN
! DIAG ENTRopy
! VIBRan NMODes 500
! DIAG
! print norm vector dipole
!mini abnr nstep 100 nprint 100 tolg 0.000000 ! target-min-step7-tolg-0_000000.crd
BOMLEV -2
open unit 1 write form name " + " \"second.dat\" " + @"
REDUce CMPAct
vibran
!diag
write second card unit 1
close unit 1
!calc natom3 ?NATOM *3
!vibran nmode @natom3
!diag
!print norm
!bomlev - 2
!VIBRan NMOD 300
!DIAGonalize
!https://www.charmm.org/charmm/documentation/by-version/c42b1/params/doc/vibran/
stop
";
conf_inp = conf_inp.Replace("$$topname$$", topname)
.Replace("$$parname$$", parname)
.Replace("$$psfname$$", psfname)
.Replace("$$crdname$$", crdname)
.Replace("$$mincrdname$$", mincrdname)
;
HFile.WriteAllText("conf.inp", conf_inp);
System.Console.WriteLine("Run the following command at " + temp + " :");
System.Console.WriteLine(" $ charmm < conf.inp");
System.Console.WriteLine(" or $ mpd&");
System.Console.WriteLine(" $ mpirun -n 38 charmm_M < conf.inp");
System.Console.WriteLine("Then, copy second.dat to " + temp);
while (true)
{
bool next = HConsole.ReadValue <bool>("Ready for next? ", false, null, false, true);
if (next)
{
if (HFile.ExistsAll(mincrdname))
{
mincrdlines = HFile.ReadAllLines(mincrdname);
/// second.dat has the following format
///
/// num-atoms
/// pot-energy
/// atom1-xforce atom1-yforce atom1-zforce
/// atom2-xforce atom2-yforce atom2-zforce
/// ...
/// atomn-xforce atomn-yforce atomn-zforce
/// upper- or lower-diag elem 1
/// upper- or lower-diag elem 2
/// ....
/// upper- or lower-diag elem 3n*3n/2
/// atom1-xcoord atom1-ycoord atom1-zcoord
/// atom2-xcoord atom2-ycoord atom2-zcoord
/// ...
/// atomn-xcoord atomn-ycoord atomn-zcoord
///
break;
}
System.Console.WriteLine("DO, copy target.psf and target.crd to " + temp);
}
}
temp.QuitTemp();
}
return(mincrdlines);
}
public static SPsfCrd BuildPsfCrd
(IEnumerable <string> toplines
, IEnumerable <string> parlines
, IEnumerable <string> pdblines
)
{
string tempbase = @"C:\temp\";
SPsfCrd psfcrd;
using (var temp = new HTempDirectory(tempbase, null))
{
temp.EnterTemp();
string topname = "top.rtf"; HFile.WriteAllLines(topname, toplines);
string parname = "par.prm"; HFile.WriteAllLines(parname, parlines);
string tgtname = "target"; HFile.WriteAllLines(tgtname + ".pdb", pdblines);
string Setup_inp = @"* Run Segment Through CHARMM
*
! read topology and parameter files
read rtf card name $$topname$$
read para card name $$parname$$
! Read sequence from the PDB coordinate file
open unit 1 card read name $$tgtname$$.pdb
read sequ pdb unit 1
! now generate the PSF and also the IC table (SETU keyword)
generate setu a-pro first NTER last CTER
rewind unit 1
! set bomlev to -1 to avois sying on lack of hydrogen coordinates
bomlev -1
read coor pdb unit 1
! them put bomlev back up to 0
bomlev 0
close unit 1
! prints out number of atoms that still have undefined coordinates.
define test select segid a-pro .and. ( .not. hydrogen ) .and. ( .not. init ) show end
ic para
ic fill preserve
ic build
hbuild sele all end
! write out the protein structure file (psf) and
! the coordinate file in pdb and crd format.
write psf card name $$tgtname$$.psf
* PSF
*
write coor card name $$tgtname$$.crd
* Coords
*
stop
"
.Replace("$$topname$$", topname)
.Replace("$$parname$$", parname)
.Replace("$$tgtname$$", tgtname);
HFile.WriteAllText("Setup.inp", Setup_inp);
System.Console.WriteLine("Run the following command at " + temp + " :");
System.Console.WriteLine(" $ charmm < Setup.inp");
System.Console.WriteLine(" or $ mpd&");
System.Console.WriteLine(" $ mpirun -n 38 charmm_M < Setup.inp");
System.Console.WriteLine("Then, copy target.psf and target.crd to " + temp);
while (true)
{
bool next = HConsole.ReadValue <bool>("Ready for next? ", false, null, false, true);
if (next)
{
if (HFile.ExistsAll("target.crd", "target.psf"))
{
string[] crdlines = HFile.ReadAllLines("target.crd");
string[] psflines = HFile.ReadAllLines("target.psf");
psfcrd = new SPsfCrd
{
crdlines = crdlines,
psflines = psflines,
};
break;
}
System.Console.WriteLine("DO, copy target.psf and target.crd to " + temp);
}
}
temp.QuitTemp();
}
return(psfcrd);
}
