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jayponderjayponder
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add AMOEBA vdwpair and polpair values for Zn+2 cation
1 parent 0c13492 commit 2d8aff9

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8 files changed

+92
-47
lines changed

8 files changed

+92
-47
lines changed

‎example/tip4p.key‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
1-
##############################################################
2-
## ##
3-
## Keyfile for TIP4P & TIP4P-Ew Rigid 4-Site Water Models ##
4-
## ##
5-
##############################################################
1+
#################################################################
2+
## ##
3+
## Keyfile for TIP4P & TIP4P-Ewald Rigid 4-Site Water Models ##
4+
## ##
5+
#################################################################
66

77
parameters NONE
88
rattle WATER
@@ -33,11 +33,11 @@ charge 1 0.000
3333
charge 2 0.520
3434
charge 3 -1.040
3535

36-
## TIP4P-Ew Parameters (J Chem Phys, 120, 9665-9678, 2004)
36+
## TIP4P-Ewald Parameters (J Chem Phys, 120, 9665-9678, 2004)
3737

38-
#atom 1 O "TIP4P-Ew O" 8 15.995 3
39-
#atom 2 H "TIP4P-Ew H" 1 1.008 1
40-
#atom 3 M "TIP4P-Ew M" 0 0.000 1
38+
#atom 1 O "TIP4P-Ewald O" 8 15.995 3
39+
#atom 2 H "TIP4P-Ewald H" 1 1.008 1
40+
#atom 3 M "TIP4P-Ewald M" 0 0.000 1
4141

4242
#bond 1 2 1000.0 0.9572
4343
#bond 1 3 1000.0 0.1250

‎example/tip4pbox.key‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -14,11 +14,11 @@ ewald-cutoff 9.0
1414
vdw-cutoff 12.0
1515
vdw-correction
1616

17-
## TIP4P-Ew Parameters (J Chem Phys, 120, 9665-9678, 2004)
17+
## TIP4P-Ewald Parameters (J Chem Phys, 120, 9665-9678, 2004)
1818

19-
atom 1 O "TIP4P-Ew O" 8 15.995 3
20-
atom 2 H "TIP4P-Ew H" 1 1.008 1
21-
atom 3 M "TIP4P-Ew M" 0 0.000 1
19+
atom 1 O "TIP4P-Ewald O" 8 15.995 3
20+
atom 2 H "TIP4P-Ewald H" 1 1.008 1
21+
atom 3 M "TIP4P-Ewald M" 0 0.000 1
2222

2323
bond 1 2 1000.0 0.9572
2424
bond 1 3 1000.0 0.1250

‎params/0README‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -128,7 +128,7 @@
128128
directional hydrogen bonding and electronegativity
129129
bond length correction terms are implemented, but
130130
the anomeric and Bohlmann correction terms are not
131-
implemented.
131+
implemented
132132

133133
mm3pro Protein-only version of the MM3 parameters; the
134134
dielectric constant and some bond stretch and torsion
@@ -148,8 +148,8 @@
148148
organic molecules
149149

150150
oplsaa24 OPLS-AA parameters based on results for a series of small
151-
organic molecules generated by the LigParGen server, and
152-
modified to provide transferable functional group values
151+
organic molecules generated by the LigParGen server, for
152+
use as templates to transfer to similar functional groups
153153

154154
oplsaal A modified version of the 1997 OPLS-AA with optimized
155155
torsional parameters for the protein backbone and side

‎params/amoebabio18.prm‎

Lines changed: 19 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -632,6 +632,10 @@ vdwpair 4 31 3.1000 0.0400
632632
vdwpair 5 98 3.0000 0.1530
633633
vdwpair 5 99 3.2700 0.1750
634634
vdwpair 5 102 2.8900 0.1750
635+
vdwpair 14 102 3.8810 0.1330
636+
vdwpair 21 102 2.7920 0.1330
637+
vdwpair 31 102 2.5190 0.1330
638+
vdwpair 37 102 2.6120 0.1330
635639
vdwpair 49 93 3.3870 0.2400
636640
vdwpair 49 94 3.6760 0.2900
637641
vdwpair 49 98 3.4250 0.2150
@@ -5712,6 +5716,21 @@ polarize 364 5.6500 0.3900
57125716
polarize 365 7.2500 0.3900
57135717

57145718

5719+
######################################
5720+
## ##
5721+
## Polarizability Pair Parameters ##
5722+
## ##
5723+
######################################
5724+
5725+
5726+
polpair 49 361 0.2840
5727+
polpair 88 361 0.2080
5728+
polpair 140 361 0.2470
5729+
polpair 158 361 0.2470
5730+
polpair 190 361 0.2010
5731+
polpair 219 361 0.2010
5732+
5733+
57155734
#####################################
57165735
## ##
57175736
## Implicit Solvation Parameters ##

‎params/amoebapro13.prm‎

Lines changed: 19 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -493,6 +493,10 @@ vdwpair 4 31 3.1000 0.0400
493493
vdwpair 5 51 3.0000 0.1530
494494
vdwpair 5 52 3.2700 0.1750
495495
vdwpair 5 55 2.8900 0.1750
496+
vdwpair 14 55 3.8810 0.1330
497+
vdwpair 21 55 2.7920 0.1330
498+
vdwpair 31 55 2.5190 0.1330
499+
vdwpair 37 55 2.6120 0.1330
496500
vdwpair 47 57 4.2360 0.1512
497501
vdwpair 47 58 4.3790 0.1664
498502
vdwpair 47 59 4.6360 0.1720
@@ -3899,6 +3903,21 @@ polarize 262 5.6500 0.3900
38993903
polarize 263 7.2500 0.3900
39003904

39013905

3906+
######################################
3907+
## ##
3908+
## Polarizability Pair Parameters ##
3909+
## ##
3910+
######################################
3911+
3912+
3913+
polpair 49 259 0.2840
3914+
polpair 88 259 0.2080
3915+
polpair 140 259 0.2470
3916+
polpair 158 259 0.2470
3917+
polpair 190 259 0.2010
3918+
polpair 219 259 0.2010
3919+
3920+
39023921
#####################################
39033922
## ##
39043923
## Implicit Solvation Parameters ##

‎source/chksymm.f‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@
1313
c
1414
c
1515
c "chksymm" examines the current coordinates for linearity,
16-
c planarity, an internal mirror plane or center of inversion
16+
c planarity, internal mirror planes or a center of inversion
1717
c
1818
c
1919
subroutine chksymm (symmtyp)

‎source/findseq.f‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -336,9 +336,9 @@ subroutine findseq
336336
c
337337
c perform deallocation of some local arrays
338338
c
339-
deallocate (list)
340339
deallocate (flink)
341340
deallocate (blink)
342341
deallocate (clink)
342+
deallocate (list)
343343
return
344344
end

‎source/testgrad.f‎

Lines changed: 36 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -31,17 +31,19 @@ program testgrad
3131
integer i,j,ixyz
3232
integer next,frame
3333
integer freeunit
34-
real*8 etot,f,f0,eps,eps0,old,energy
35-
real*8 eb0,ea0,eba0,eub0,eaa0,eopb0
36-
real*8 eopd0,eid0,eit0,et0,ept0,ebt0
37-
real*8 eat0,ett0,ev0,er0,edsp0,ec0
38-
real*8 ecd0,ed0,em0,ep0,ect0,erxf0
34+
real*8 eval,energy
35+
real*8 f,f0,eps,eps0,old
36+
real*8 eb0,ea0,eba0,eub0
37+
real*8 eaa0,eopb0,eopd0,eid0
38+
real*8 eit0,et0,ept0,ebt0
39+
real*8 eat0,ett0,ev0,er0
40+
real*8 edsp0,ec0,ecd0,ed0
41+
real*8 em0,ep0,ect0,erxf0
3942
real*8 es0,elf0,eg0,ex0
4043
real*8 totnorm,ntotnorm,rms,nrms
4144
real*8, allocatable :: denorm(:)
4245
real*8, allocatable :: ndenorm(:)
43-
real*8, allocatable :: detot(:,:)
44-
real*8, allocatable :: ndetot(:,:)
46+
real*8, allocatable :: ndesum(:,:)
4547
real*8, allocatable :: ndeb(:,:)
4648
real*8, allocatable :: ndea(:,:)
4749
real*8, allocatable :: ndeba(:,:)
@@ -70,6 +72,7 @@ program testgrad
7072
real*8, allocatable :: ndelf(:,:)
7173
real*8, allocatable :: ndeg(:,:)
7274
real*8, allocatable :: ndex(:,:)
75+
real*8, allocatable :: derivs(:,:)
7376
logical exist,query
7477
logical doanalyt,donumer,dofull
7578
character*1 answer
@@ -170,11 +173,13 @@ program testgrad
170173
c
171174
c perform dynamic allocation of some local arrays
172175
c
173-
allocate (denorm(n))
174-
allocate (detot(3,n))
176+
if (doanalyt) then
177+
allocate (denorm(n))
178+
allocate (derivs(3,n))
179+
end if
175180
if (donumer) then
176181
allocate (ndenorm(n))
177-
allocate (ndetot(3,n))
182+
allocate (ndesum(3,n))
178183
allocate (ndeb(3,n))
179184
allocate (ndea(3,n))
180185
allocate (ndeba(3,n))
@@ -214,25 +219,25 @@ program testgrad
214219
100 format (/,' Analysis for Archive Structure :',8x,i8)
215220
end if
216221
c
217-
c compute the analytical gradient components
222+
c compute the energy and analytical gradient components
218223
c
219224
if (doanalyt) then
220-
call gradient (etot,detot)
225+
call gradient (eval,derivs)
221226
end if
222227
c
223228
c print the total potential energy of the system
224229
c
225230
if (doanalyt) then
226231
if (digits .ge. 8) then
227-
write (iout,110) etot
232+
write (iout,110) esum
228233
110 format (/,' Total Potential Energy :',8x,f20.8,
229234
& ' Kcal/mole')
230235
else if (digits .ge. 6) then
231-
write (iout,120) etot
236+
write (iout,120) esum
232237
120 format (/,' Total Potential Energy :',8x,f18.6,
233238
& ' Kcal/mole')
234239
else
235-
write (iout,130) etot
240+
write (iout,130) esum
236241
130 format (/,' Total Potential Energy :',8x,f16.4,
237242
& ' Kcal/mole')
238243
end if
@@ -399,7 +404,7 @@ program testgrad
399404
else if (j .eq. 3) then
400405
z(i) = old
401406
end if
402-
ndetot(j,i) = (f - f0) / eps
407+
ndesum(j,i) = (f - f0) / eps
403408
ndeb(j,i) = (eb - eb0) / eps
404409
ndea(j,i) = (ea - ea0) / eps
405410
ndeba(j,i) = (eba - eba0) / eps
@@ -574,34 +579,34 @@ program testgrad
574579
ntotnorm = 0.0d0
575580
do i = 1, n
576581
if (doanalyt .and. use(i)) then
577-
denorm(i) = detot(1,i)**2 + detot(2,i)**2
578-
& + detot(3,i)**2
582+
denorm(i) = desum(1,i)**2 + desum(2,i)**2
583+
& + desum(3,i)**2
579584
totnorm = totnorm + denorm(i)
580585
denorm(i) = sqrt(denorm(i))
581586
if (digits .ge. 8) then
582-
write (iout,350) i,(detot(j,i),j=1,3),denorm(i)
587+
write (iout,350) i,(desum(j,i),j=1,3),denorm(i)
583588
350 format (' Anlyt',i8,1x,3f16.8,f16.8)
584589
else if (digits .ge. 6) then
585-
write (iout,360) i,(detot(j,i),j=1,3),denorm(i)
590+
write (iout,360) i,(desum(j,i),j=1,3),denorm(i)
586591
360 format (' Anlyt',2x,i8,3x,3f14.6,2x,f14.6)
587592
else
588-
write (iout,370) i,(detot(j,i),j=1,3),denorm(i)
593+
write (iout,370) i,(desum(j,i),j=1,3),denorm(i)
589594
370 format (' Anlyt',2x,i8,7x,3f12.4,2x,f12.4)
590595
end if
591596
end if
592597
if (donumer .and. use(i)) then
593-
ndenorm(i) = ndetot(1,i)**2 + ndetot(2,i)**2
594-
& + ndetot(3,i)**2
598+
ndenorm(i) = ndesum(1,i)**2 + ndesum(2,i)**2
599+
& + ndesum(3,i)**2
595600
ntotnorm = ntotnorm + ndenorm(i)
596601
ndenorm(i) = sqrt(ndenorm(i))
597602
if (digits .ge. 8) then
598-
write (iout,380) i,(ndetot(j,i),j=1,3),ndenorm(i)
603+
write (iout,380) i,(ndesum(j,i),j=1,3),ndenorm(i)
599604
380 format (' Numer',i8,1x,3f16.8,f16.8)
600605
else if (digits .ge. 6) then
601-
write (iout,390) i,(ndetot(j,i),j=1,3),ndenorm(i)
606+
write (iout,390) i,(ndesum(j,i),j=1,3),ndenorm(i)
602607
390 format (' Numer',2x,i8,3x,3f14.6,2x,f14.6)
603608
else
604-
write (iout,400) i,(ndetot(j,i),j=1,3),ndenorm(i)
609+
write (iout,400) i,(ndesum(j,i),j=1,3),ndenorm(i)
605610
400 format (' Numer',2x,i8,7x,3f12.4,2x,f12.4)
606611
end if
607612
end if
@@ -699,11 +704,13 @@ program testgrad
699704
c
700705
c perform deallocation of some local arrays
701706
c
702-
deallocate (denorm)
703-
deallocate (detot)
707+
if (doanalyt) then
708+
deallocate (denorm)
709+
deallocate (derivs)
710+
end if
704711
if (donumer) then
705712
deallocate (ndenorm)
706-
deallocate (ndetot)
713+
deallocate (ndesum)
707714
deallocate (ndeb)
708715
deallocate (ndea)
709716
deallocate (ndeba)

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