3.992146 3.451319 2.676042 3.353784
4.172640 2.402115 2.402115
- -61.60000 -35.26000 3.800125 48.12500
- 35.00000 2.916757 3.655463 4.547977
+ -7.2938 -4.0239 3.800125 5.9101
+ 3.8743 2.916757 3.655463 4.547977
2.618191 2.618191
- -23.62500 3.505321 39.90000 28.44000
+ -3.0057 3.505321 6.0636 3.5303
2.690483 3.371882 4.195157 2.415078
2.415078
3.824000 4.378585 3.785405 2.935082
3.678429 4.576550 2.634640 2.634640
- -1.447000 -28.07000 3.360749 4.211903
+ -0.1779 −3.4493 3.360749 4.211903
5.240276 3.016734 3.016734
- -76.82000 2.905459 3.641304 4.530360
+ -6.5557 2.905459 3.641304 4.530360
2.608049 2.608049
2.252800 2.823350 3.512697 2.022197
.0572167103 -.0468608825 .0151048455 .0084963678
.0278930397 .0076922911 .1033536738 -.0098256036
.0611385674 .0448303346 .0861379100 .0861379100
+
2.252000 2.758289 2.828747 2.573807
2.573807 2.314337 3.329045 3.123838
1.679138 1.245463 2.417517 2.138542
3.178800 3.464740 3.195954 3.486507
3.992146 3.451319 2.676042 3.353784
4.172640 2.402115 2.402115
-
- -61.60000 -35.26000 3.800125 48.12500
- 35.00000 2.916757 3.655463 4.547977
- 2.618191 2.618191
-
- -23.62500 3.505321 39.90000 28.44000
- 2.690483 3.371882 4.195157 2.415078
- 2.415078
-
- 3.824000 4.378585 3.785405 2.935082
- 3.678429 4.576550 2.634640 2.634640
-
- -1.447000 -28.07000 3.360749 4.211903
- 5.240276 3.016734 3.016734
-
- -76.82000 2.905459 3.641304 4.530360
- 2.608049 2.608049
-
- 2.252800 2.823350 3.512697 2.022197
- 2.022197
-
- 3.538400 4.402332 2.534345 2.534345
-
- 5.477200 3.153127 3.153127
-
- 1.815200 1.815200
-
- 1.815200
-
+
+ -7.2938 -4.0239 3.800125 5.9101
+ 3.8743 2.916757 3.655463 4.547977
+ 2.618191 2.618191
+
+ -3.0057 3.505321 6.0636 3.5303
+ 2.690483 3.371882 4.195157 2.415078
+ 2.415078
+
+ 3.824000 4.378585 3.785405 2.935082
+ 3.678429 4.576550 2.634640 2.634640
+
+ -0.1779 -3.4493 3.360749 4.211903
+ 5.240276 3.016734 3.016734
+
+ -6.5557 2.905459 3.641304 4.530360
+ 2.608049 2.608049
+
+ 2.252800 2.823350 3.512697 2.022197
+ 2.022197
+
+ 3.538400 4.402332 2.534345 2.534345
+
+ 5.477200 3.153127 3.153127
+
+ 1.815200 1.815200
+
+ 1.815200
+
& +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
& +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+C write(iout,*) "tu,", i,j,aa_lip(itypi,itypj),bb_lip(itypi,itypj)
C if (aa.ne.aa_aq(itypi,itypj)) write(63,'(2e10.5)')
C &(aa-aa_aq(itypi,itypj)),(bb-bb_aq(itypi,itypj))
C if (ssgradlipj.gt.0.0d0) print *,"??WTF??"
& +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
C if (aa.ne.aa_aq(itypi,itypj)) write(63,'2e10.5')
C &(aa-aa_aq(itypi,itypj)),(bb-bb_aq(itypi,itypj))
+C write(iout,*) "tu,", i,j,aa,bb,aa_lip(itypi,itypj),sslipi,sslipj
dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
xj_safe=xj
yj_safe=yj
if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then
C YES vbldpDUM is the equlibrium length of spring for Dummy atom
diff = vbld(i)-vbldpDUM
+ if (energy_dec) write(iout,*) "dum_bond",i,diff
else
C NO vbldp0 is the equlibrium lenght of spring for peptide group
diff = vbld(i)-vbldp0
c write (iout,'(i5,3f10.5)') i,(gradb(j,i-1),j=1,3)
c endif
enddo
+
estr=0.5d0*AKP*estr+estr1
c
c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
if (itype(i).eq.ntyp1) cycle
positi=(mod(((c(3,i)+c(3,i+1))/2.0d0),boxzsize))
- if (positi.le.0) positi=positi+boxzsize
+ if (positi.le.0.0) positi=positi+boxzsize
C print *,i
C first for peptide groups
c for each residue check if it is in lipid or lipid water border area
C now we start reading lipid
do i=1,ntyp
read (isidep,*,end=1161,err=1161)(epslip(i,j),j=i,ntyp)
+ write(iout,*) "epslip", i, (epslip(i,j),j=i,ntyp)
+
C print *,"WARNING!!"
C do j=1,ntyp
C epslip(i,j)=epslip(i,j)+0.05d0
include 'COMMON.SBRIDGE'
logical lprn
common /srutu/icall
- integer icant
+ integer icant,xshift,yshift,zshift
external icant
do i=1,210
do j=1,2
& +aa_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
bb=bb_lip(itypi,itypj)*(sslipi+sslipj)/2.0d0
& +bb_aq(itypi,itypj)*(2.0d0-sslipi-sslipj)/2.0d0
+C write(iout,*) "tu,", i,j,aa_lip(itypi,itypj),bb_lip(itypi,itypj)
+
C write(iout,*),aa,aa_lip(itypi,itypj),aa_aq(itypi,itypj)
C checking the distance
dist_init=(xj-xi)**2+(yj-yi)**2+(zj-zi)**2
gcorr_loc(i)=0.0d0
enddo
do i=iatel_s,iatel_e
- if (i.eq.1) then
+C if (i.eq.1) then
if (itype(i).eq.ntyp1.or. itype(i+1).eq.ntyp1
- & .or. itype(i+2).eq.ntyp1) cycle
- else
- if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
- & .or. itype(i+2).eq.ntyp1
- & .or. itype(i-1).eq.ntyp1
+C & .or. itype(i+2).eq.ntyp1) cycle
+C else
+C if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
+C & .or. itype(i+2).eq.ntyp1
+C & .or. itype(i-1).eq.ntyp1
&) cycle
- endif
+C endif
if (itel(i).eq.0) goto 1215
dxi=dc(1,i)
dyi=dc(2,i)
num_conti=0
C write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
do j=ielstart(i),ielend(i)
- if (j.eq.1) then
- if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1
- & .or.itype(j+2).eq.ntyp1
- &) cycle
- else
+ if (j.le.1) cycle
+C if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1
+C & .or.itype(j+2).eq.ntyp1
+C &) cycle
+C else
if (itype(j).eq.ntyp1 .or. itype(j+1).eq.ntyp1
- & .or.itype(j+2).eq.ntyp1
- & .or.itype(j-1).eq.ntyp1
+C & .or.itype(j+2).eq.ntyp1
+C & .or.itype(j-1).eq.ntyp1
&) cycle
- endif
+C endif
C
C) cycle
if (itel(j).eq.0) goto 1216
& aggj(3,4),aggj1(3,4),a_temp(2,2)
common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,j1,j2
if (j.eq.i+2) then
+ if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
+C changes suggested by Ana to avoid out of bounds
+C & .or.((i+5).gt.nres)
+C & .or.((i-1).le.0)
+C end of changes suggested by Ana
+ & .or. itype(i+2).eq.ntyp1
+ & .or. itype(i+3).eq.ntyp1
+C & .or. itype(i+5).eq.ntyp1
+C & .or. itype(i).eq.ntyp1
+C & .or. itype(i-1).eq.ntyp1
+ & ) goto 178
+
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C Third-order contributions
else if (j.eq.i+3 .and. itype(i+2).ne.ntyp1) then
if (itype(i).eq.ntyp1 .or. itype(i+1).eq.ntyp1
C changes suggested by Ana to avoid out of bounds
- & .or.((i+5).gt.nres)
- & .or.((i-1).le.0)
+C & .or.((i+5).gt.nres)
+C & .or.((i-1).le.0)
C end of changes suggested by Ana
& .or. itype(i+3).eq.ntyp1
& .or. itype(i+4).eq.ntyp1
- & .or. itype(i+5).eq.ntyp1
+C & .or. itype(i+5).eq.ntyp1
& .or. itype(i).eq.ntyp1
- & .or. itype(i-1).eq.ntyp1) goto 178
+C & .or. itype(i-1).eq.ntyp1
+ & ) goto 178
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
C
C Fourth-order contributions
C else
if (itype(i-1).eq.ntyp1 .or. itype(i).eq.ntyp1) then
diff = vbld(i)-vbldpDUM
+C write(iout,*) i,diff
else
diff = vbld(i)-vbldp0
c write (iout,*) i,vbld(i),vbldp0,diff,AKP*diff*diff
read (isidep,*)(alp(i),i=1,ntyp)
do i=1,ntyp
read (isidep,*)(epslip(i,j),j=i,ntyp)
-C print *,"WARNING!!"
+C write(iout,*) "WARNING!!",i,ntyp
+ write(iout,*) "epslip", i, (epslip(i,j),j=i,ntyp)
C do j=1,ntyp
C epslip(i,j)=epslip(i,j)+0.05d0
C enddo
do iparm=1,nParmSet
#ifdef DEBUG
write (iout,'(2i5,21f8.2)') i,iparm,
- & (enetb(k,i,iparm),k=1,21)
+ & (enetb(k,i,iparm),k=1,22)
#endif
call restore_parm(iparm)
#ifdef DEBUG