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update output format of implicit solvation parameters
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@jayponder
jayponder committed May 7, 2024
1 parent 2e2a2ae commit ecbd929
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2 changes: 1 addition & 1 deletion example/diene.key
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@@ -1,3 +1,3 @@
parameters ../params/mm3
pisystem 1 2 3 4
pisystem 1 2 3 4
verbose
3 changes: 3 additions & 0 deletions example/lysozyme.key
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@@ -0,0 +1,3 @@
parameters ../params/amoebabio18
verbose
solvate GK
4,694 changes: 4,694 additions & 0 deletions example/lysozyme.pdb
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9 changes: 9 additions & 0 deletions example/lysozyme.seq
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A 1 LYS VAL PHE GLY ARG CYX GLU LEU ALA ALA ALA MET LYS ARG HIS
A 16 GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY ASN TRP VAL CYX
A 31 ALA ALA LYS PHE GLU SER ASN PHE ASN THR GLN ALA THR ASN ARG
A 46 ASN THR ASP GLY SER THR ASP TYR GLY ILE LEU GLN ILE ASN SER
A 61 ARG TRP TRP CYX ASN ASP GLY ARG THR PRO GLY SER ARG ASN LEU
A 76 CYX ASN ILE PRO CYX SER ALA LEU LEU SER SER ASP ILE THR ALA
A 91 SER VAL ASN CYX ALA LYS LYS ILE VAL SER ASP GLY ASN GLY MET
A 106 ASN ALA TRP VAL ALA TRP ARG ASN ARG CYX LYS GLY THR ASP VAL
A 121 GLN ALA TRP ILE ARG GLY CYX ARG LEU
2,430 changes: 2,430 additions & 0 deletions example/lysozyme.xyz
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4 changes: 2 additions & 2 deletions example/water.key
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@@ -1,2 +1,2 @@
parameters ../params/water03
#parameters ../params/hippo19
parameters ../params/water03
#parameters ../params/hippo19
42 changes: 28 additions & 14 deletions source/analyze.f
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Expand Up @@ -1232,6 +1232,7 @@ subroutine paramyze (active)
use polpot
use potent
use repel
use solpot
use solute
use strbnd
use strtor
Expand Down Expand Up @@ -2172,13 +2173,26 @@ subroutine paramyze (active)
k = k + 1
if (header) then
header = .false.
write (iout,980)
980 format (/,' Implicit Solvation Parameters :',
& //,10x,'Atom Number',13x,'Radius',
& 3x,'ASP Value',/)
if (solvtyp(1:2).eq.'PB' .or.
& solvtyp(1:2).eq.'GK') then
write (iout,980)
980 format (/,' Implicit Solvation Parameters :',
& //,10x,'Atom Number',13x,'Radius',
& 3x,'Surface',4x,'S-Neck',/)
else
write (iout,990)
990 format (/,' Implicit Solvation Parameters :',
& //,10x,'Atom Number',13x,'Radius',
& 3x,'Surface',/)
end if
end if
if (solvtyp(1:2).eq.'PB' .or. solvtyp(1:2).eq.'GK') then
write (iout,1000) k,i,rsolv(i),asolv(i),sneck(i)
1000 format (i6,3x,i6,15x,3f10.4)
else
write (iout,1010) k,i,rsolv(i),asolv(i)
1010 format (i6,3x,i6,15x,2f10.4)
end if
write (iout,990) k,i,rsolv(i),asolv(i)
990 format (i6,3x,i6,15x,2f10.4)
end if
end do
end if
Expand All @@ -2192,13 +2206,13 @@ subroutine paramyze (active)
j = class(ia)
if (header) then
header = .false.
write (iout,1000)
1000 format (/,' Conjugated Pi-Atom Parameters :',
write (iout,1020)
1020 format (/,' Conjugated Pi-Atom Parameters :',
& //,10x,'Atom Number',14x,'Nelect',
& 6x,'Ionize',4x,'Repulsion',/)
end if
write (iout,1010) i,ia,electron(j),ionize(j),repulse(j)
1010 format (i6,3x,i6,17x,f8.1,3x,f10.4,2x,f10.4)
write (iout,1030) i,ia,electron(j),ionize(j),repulse(j)
1030 format (i6,3x,i6,17x,f8.1,3x,f10.4,2x,f10.4)
end do
end if
c
Expand All @@ -2211,13 +2225,13 @@ subroutine paramyze (active)
ib = ibpi(3,i)
if (header) then
header = .false.
write (iout,1020)
1020 format (/,' Conjugated Pi-Bond Parameters :',
write (iout,1040)
1040 format (/,' Conjugated Pi-Bond Parameters :',
& //,10x,'Atom Numbers',21x,'K Slope',
& 3x,'L Slope',/)
end if
write (iout,1030) i,ia,ib,kslope(i),lslope(i)
1030 format (i6,3x,2i6,19x,2f10.4)
write (iout,1050) i,ia,ib,kslope(i),lslope(i)
1050 format (i6,3x,2i6,19x,2f10.4)
end do
end if
return
Expand Down
10 changes: 5 additions & 5 deletions source/ksolv.f
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Expand Up @@ -159,16 +159,16 @@ subroutine ksolv
header = .false.
write (iout,30)
30 format (/,' Additional Solvation Parameters :',
& //,5x,'Atom Type',16x,'PB Size',5x,'CS Size',
& //,5x,'Atom Type',13x,'PB Size',5x,'CS Size',
& 5x,'GK Size',6x,'S-Neck',/)
end if
pbr(k) = pbrd
gkr(k) = csrd
pbr(k) = gkrd
pbr(k) = 0.5d0 * pbrd
csr(k) = 0.5d0 * csrd
gkr(k) = 0.5d0 * gkrd
snk(k) = snek
if (.not. silent) then
write (iout,40) k,pbrd,csrd,gkrd,snek
40 format (6x,i6,7x,4f12.4)
40 format (6x,i6,10x,4f12.4)
end if
else if (k .gt. maxtyp) then
write (iout,50) maxtyp
Expand Down
10 changes: 5 additions & 5 deletions source/surfatom.f
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Expand Up @@ -652,7 +652,7 @@ subroutine surfatom1 (ir,area,darea,radius)
c
if (io .ge. maxarc) then
write (iout,20)
20 format (/,' SURFATOM -- Increase the Value of MAXARC')
20 format (/,' SURFATOM1 -- Increase the Value of MAXARC')
call fatal
end if
c
Expand Down Expand Up @@ -862,7 +862,7 @@ subroutine surfatom1 (ir,area,darea,radius)
narc = narc + 1
if (narc .ge. maxarc) then
write (iout,70)
70 format (/,' SURFATOM -- Increase the Value',
70 format (/,' SURFATOM1 -- Increase the Value',
& ' of MAXARC')
call fatal
end if
Expand Down Expand Up @@ -907,7 +907,7 @@ subroutine surfatom1 (ir,area,darea,radius)
jb = jb + 1
if (jb .ge. maxarc) then
write (iout,80)
80 format (/,' SURFATOM -- Increase the Value',
80 format (/,' SURFATOM1 -- Increase the Value',
& ' of MAXARC')
call fatal
end if
Expand Down Expand Up @@ -1044,7 +1044,7 @@ subroutine surfatom1 (ir,area,darea,radius)
c
if (moved) then
write (iout,140) ir
140 format (/,' SURFATOM -- Connectivity Error at Atom',i6)
140 format (/,' SURFATOM1 -- Connectivity Error at Atom',i6)
else
moved = .true.
xr = xr + rmove
Expand All @@ -1064,7 +1064,7 @@ subroutine surfatom1 (ir,area,darea,radius)
if (area .lt. 0.0d0) then
if (moved) then
write (iout,160) ir
160 format (/,' SURFATOM -- Negative Area at Atom',i6)
160 format (/,' SURFATOM1 -- Negative Area at Atom',i6)
else
moved = .true.
xr = xr + rmove
Expand Down

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