I have total 256 water molecules. I am trying to genrate the .top file from .pdb so I used pdb2gmx.
How can I genrate the .top file with pdb2gmx for 256 water molecules. Nilesh On Tue, April 26, 2011 1:01 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello, >> >> >> I am trying to run a simulation for flexiable water. I use the >> parameters from J. Chem. Phys. (2006),124,024503 paper and made floowing >> changes. >> >> I addes "WAT" as a new residue name in aminoacids.dat >> >> >> I addred two atom times in ffoplsaa.atp >> >> >> opls_1001 15.99940 ; O SPC_fw Water opls_1002 1.00800 ; H SPC_fw >> Water >> >> >> >> I added following parameters in ffoplsaa.rtp >> >> >> [ WAT] >> [ atoms ] >> OWA opls_1001 -0.82 1 >> HWA1 opls_1002 0.41 2 >> HWA2 opls_1002 0.41 2 >> >> >> [ bonds ] >> OWA HWA1 >> OWA HWA2 >> >> >> I made a spc_fw.itp file. >> >> >> ; Derived from parsing of runfiles/alat.top.orig >> [ defaults ] >> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ >> ;1 3 yes 0.5 0.5 >> ; comb-rule 3 is square-root sigma, the OPLSAA version >> >> >> [ atomtypes ] >> ; full atom descriptions are available in ffoplsaa.atp >> ; name bond_type mass charge ptype sigma epsilon >> opls_1001 OWA 8 15.99940 -0.820 A 3.1655e-01 >> 6.503e-01 >> opls_1002 HWA 1 1.00800 0.410 A 0.00e+00 0.00e+00 >> >> [ bondtypes ] >> ; i j func b0 kb >> OWA HWA 1 0.1012 443153.3808 ; J. Chem. Phys. >> (2006),124,024503 >> >> >> >> [ angletypes ] >> ; i j k func th0 cth >> HWA OWA HWA 1 113.24 317.5656 ; J. Chem. Phys. >> (2006),124,024503 >> >> >> [ moleculetype ] >> ; Name nrexcl >> WAT 3 >> >> >> [ atoms ] >> >> >> ; nr type resnr residue atom cgnr charge mass >> typeB chargeB massB 1 opls_1001 1 WAT OWA 1 >> -0.82 >> 2 opls_1002 1 WAT HWA1 1 0.41 >> 3 opls_1002 1 WAT HWA2 1 0.41 >> >> >> [ bonds ] >> ; i j funct >> 1 2 1 >> 1 3 1 >> >> >> >> [ angles ] >> ; i j k funct >> 2 1 3 1 >> >> >> >> Finally I made changes in ffoplsaa.itp file >> >> >> ;#include "ffoplsaanb.itp" >> ;#include "ffoplsaabon.itp" >> #include "spc_fw.itp" >> #include "spc_fw_mol.itp" >> >> >> For pdb2gmx >> >> >> pdb2gmx -f water.pdb -o water.pdb -p water.top -ter >> >> I get following error >> >> >> Fatal error: >> Atom OWA in residue HOH 1 not found in rtp entry with 3 atoms >> while sorting atoms >> >> >> WHy is reading HOH residue. In my pdb file I mentioned WAT as residure. >> >> >> How can I fix this error? >> >> > > If I recall, pdb2gmx does some internal translations to standardize water > nomenclature. In reality, you don't need pdb2gmx at all - you've > already shown that you're created a topology for the water model. > > -Justin > > > -- > ======================================== > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists