From 6f352fb19a065386a573d715b09235bbdcfdd744 Mon Sep 17 00:00:00 2001 From: Adam Sieradzan Date: Wed, 19 Oct 2016 19:25:25 +0200 Subject: [PATCH] adding some param and control --- ...arm.1e0l_1enh_iter1-a_hier4_gap4_cum_shan10dcvr | 43 ++++ ..._GB_opt.1e0l_1enh_iter7_shance5a_class9_exp_q12 | 244 ++++++++++++++++++++ source/unres/src_MD-M/COMMON.CONTROL | 4 +- source/unres/src_MD-M/readrtns_CSA.F | 47 +++- 4 files changed, 329 insertions(+), 9 deletions(-) create mode 100644 PARAM/fourier_opt.parm.1e0l_1enh_iter1-a_hier4_gap4_cum_shan10dcvr create mode 100644 PARAM/sc_GB_opt.1e0l_1enh_iter7_shance5a_class9_exp_q12 diff --git a/PARAM/fourier_opt.parm.1e0l_1enh_iter1-a_hier4_gap4_cum_shan10dcvr b/PARAM/fourier_opt.parm.1e0l_1enh_iter1-a_hier4_gap4_cum_shan10dcvr new file mode 100644 index 0000000..1d0f10d --- /dev/null +++ b/PARAM/fourier_opt.parm.1e0l_1enh_iter1-a_hier4_gap4_cum_shan10dcvr @@ -0,0 +1,43 @@ + 3 # Number of local interaction types +Gly + 0.000000000000000 + 0.776612667116258 + 0.180007406197395 + 0.000000000000000 + 0.000000000000000 + 2.373462483972307 + -0.927962753087420 + 0.000000000000000 + 0.000000000000000 + 1.232391086511693 + -0.301309665878693 + 0.000000000000000 + 0.000000000000000 +Ala + 0.000000000000000 + 0.534534859728887 + -0.234499595726854 + -0.856605364096114 + 1.592444452734509 + -2.089734050079038 + 2.302365702770721 + -0.532502145482045 + -1.596421505165690 + 1.270742391163819 + 0.383344846384444 + -0.581625032727691 + 0.383892980467839 +Pro + 0.000000000000000 + -1.217990763570525 + 0.036014872658386 + -0.667781476044440 + 1.059569618849567 + -1.548870000000000 + 1.914370000000000 + 0.664143000000000 + -0.454839000000000 + 0.237257741258620 + -0.031285714826026 + 0.354501398699034 + 0.081897733096335 diff --git a/PARAM/sc_GB_opt.1e0l_1enh_iter7_shance5a_class9_exp_q12 b/PARAM/sc_GB_opt.1e0l_1enh_iter7_shance5a_class9_exp_q12 new file mode 100644 index 0000000..45578fd --- /dev/null +++ b/PARAM/sc_GB_opt.1e0l_1enh_iter7_shance5a_class9_exp_q12 @@ -0,0 +1,244 @@ + 4 6 + 5.605353726100000 6.220003215400000 6.215989849600000 6.438696896300000 + 6.209810123100000 5.959637479800000 5.431022266200000 4.879008525700000 + 5.263842382200000 5.496195412400000 4.292812416200000 4.358225054000000 + 4.266775592100000 3.681384595800000 3.540542964700000 3.702698591200000 + 4.717759615600000 3.381199222700000 3.793608545800000 4.515749058500000 + 6.2200032154 6.2159898496 5.2638423822 5.2638423822 + + 6.629674668000000 3.150620062861662 7.021009944667282 6.197761691273066 + 5.079780322392677 6.142519242300000 3.895977826090467 3.057887459769197 + 4.695739836899391 3.045226338330234 3.660543430110947 4.906165445263210 + 2.791642552603660 1.621110272900719 2.799574419300000 4.816426855300000 + 2.370674949270219 3.884912182904534 4.645743255500000 6.6296746680 + 6.6717260508 5.4858936024 5.4858936024 + + 2.613142542740431 2.318945555910309 4.468617361684211 2.609656795312243 + 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a/source/unres/src_MD-M/COMMON.CONTROL b/source/unres/src_MD-M/COMMON.CONTROL index 88d7571..c27bec8 100644 --- a/source/unres/src_MD-M/COMMON.CONTROL +++ b/source/unres/src_MD-M/COMMON.CONTROL @@ -1,6 +1,6 @@ integer modecalc,iscode,indpdb,indback,indphi,iranconf,icheckgrad, & inprint,i2ndstr,mucadyn,constr_dist,symetr,AFMlog,selfguide, - & shield_mode,tor_mode,tubelog + & shield_mode,tor_mode,tubelog,genconstr logical minim,refstr,pdbref,outpdb,outmol2,overlapsc,energy_dec, & sideadd,lsecondary,read_cart,unres_pdb, & vdisulf,searchsc,lmuca,dccart,extconf,out1file, @@ -11,7 +11,7 @@ & icheckgrad,minim,i2ndstr,refstr,pdbref,outpdb,outmol2,iprint, & overlapsc,energy_dec,sideadd,lsecondary,read_cart,unres_pdb & ,vdisulf,searchsc,lmuca,dccart,mucadyn,extconf,out1file, - & selfguide,AFMlog,shield_mode,tor_mode,tubelog, + & selfguide,AFMlog,shield_mode,tor_mode,tubelog,genconstr, & constr_dist,gnorm_check,gradout,split_ene,with_theta_constr, & symetr C... minim = .true. means DO minimization. diff --git a/source/unres/src_MD-M/readrtns_CSA.F b/source/unres/src_MD-M/readrtns_CSA.F index d0c10c7..fa4c75a 100644 --- a/source/unres/src_MD-M/readrtns_CSA.F +++ b/source/unres/src_MD-M/readrtns_CSA.F @@ -147,6 +147,8 @@ C constrains on theta angles WITH_THETA_CONSTR is the keyword print *,'AFMlog',AFMlog,selfguide,"KUPA" call readi(controlcard,'TUBEMOD',tubelog,0) write (iout,*) TUBElog,"TUBEMODE" + call readi(controlcard,'GENCONSTR',genconstr,0) +C write (iout,*) TUBElog,"TUBEMODE" call readi(controlcard,'IPRINT',iprint,0) C SHIELD keyword sets if the shielding effect of side-chains is used C 0 denots no shielding is used all peptide are equally despite the @@ -789,12 +791,12 @@ C 12/1/95 Added weight for the multi-body term WCORR if (dyn_ss) then ss_depth=ebr/wsc-0.25*eps(1,1) Ht=Ht/wsc-0.25*eps(1,1) - akcm=akcm*wstrain/wsc - akth=akth*wstrain/wsc - akct=akct*wstrain/wsc - v1ss=v1ss*wstrain/wsc - v2ss=v2ss*wstrain/wsc - v3ss=v3ss*wstrain/wsc + akcm=akcm/wsc + akth=akth/wsc + akct=akct/wsc + v1ss=v1ss/wsc + v2ss=v2ss/wsc + v3ss=v3ss/wsc else if (wstrain.ne.0.0) then ss_depth=ebr/wstrain-0.25*eps(1,1)*wsc/wstrain @@ -1527,6 +1529,31 @@ cd print *,'gen_dist_constr: nnt=',nnt,' nct=',nct cd write (2,*) 'gen_dist_constr: nnt=',nnt,' nct=',nct, cd & ' nstart_sup',nstart_sup,' nstart_seq',nstart_seq, cd & ' nsup',nsup + if (constr_dist.eq.11) then + do i=nstart_sup,nstart_sup+nsup-1 + do j=i+2,nstart_sup+nsup-1 + distance=dist(i,j) + if (distance.le.15.0) then + nhpb=nhpb+1 + ihpb(nhpb)=i+nstart_seq-nstart_sup + jhpb(nhpb)=j+nstart_seq-nstart_sup + forcon(nhpb)=sqrt(0.04*distance) + fordepth(nhpb)=sqrt(40.0/distance) + dhpb(nhpb)=distance-0.1d0 + dhpb1(nhpb)=distance+0.1d0 + +#ifdef MPI + if (.not.out1file .or. me.eq.king) + & write (iout,'(a,3i5,f8.2,f10.2)') "+dist.constr ", + & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) +#else + write (iout,'(a,3i5,f8.2,f10.2)') "+dist.constr ", + & nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb) +#endif + endif + enddo + enddo + else do i=nstart_sup,nstart_sup+nsup-1 cd write (2,*) 'i',i,' seq ',restyp(itype(i+nstart_seq-nstart_sup)), cd & ' seq_pdb', restyp(itype_pdb(i)) @@ -1537,7 +1564,8 @@ cd & ' seq_pdb', restyp(itype_pdb(i)) forcon(nhpb)=weidis dhpb(nhpb)=dist(i,j) enddo - enddo + enddo + endif cd write (iout,'(a)') 'Distance constraints:' cd do i=nss+1,nhpb cd ii=ihpb(i) @@ -2456,6 +2484,10 @@ c------------------------------------------------------------------------------- write (iout,*) "Calling read_dist_constr" c write (iout,*) "nres",nres," nstart_sup",nstart_sup," nsup",nsup c call flush(iout) + if ((genconstr.gt.0).and.(constr_dist.eq.11)) then + call gen_dist_constr + go to 1712 + endif call card_concat(controlcard) call readi(controlcard,"NFRAG",nfrag_,0) call readi(controlcard,"NPAIR",npair_,0) @@ -2581,6 +2613,7 @@ C dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb)) #endif enddo + 1712 continue call flush(iout) return end -- 1.7.9.5