Re: [gmx-users] Error while doing EM in DMSO.
Anil Kumar wrote: Dear Users, First of all thank you Mark, yes you are right. it was problem of force field and topoloy file mismatch. I have made changes in the ffG43a1 residue toplogy file for DMSO., but still getting the same error. Please let me know if i am doing some mistake. If the problem is the missing masses, then just add them in the [atoms] section. (Chapter 5) -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Error while doing EM in DMSO.
Dear Users, First of all thank you Mark, yes you are right. it was problem of force field and topoloy file mismatch. I have made changes in the ffG43a1 residue toplogy file for DMSO., but still getting the same error. Please let me know if i am doing some mistake. ***changes made*** [ DMSO ] [ atoms ] SD SD 0.13900 0 OD OD-0.45900 0 CD1 CD 0.16000 0 CD2 CD 0.16000 0 [ bonds ] SD ODgb_38 SD CD1gb_39 SD CD2gb_39 OD CD1gb_44 OD CD2gb_44 CD1 CD2gb_45 [ angles ] ; aiajak gromos type [ impropers ] ; aiajakal gromos type [ dihedrals ] ; aiajakal gromos type *DMSO before changes** [ DMSO ] [ atoms ] SDmso SDMSO 0.13900 0 ODmso ODMSO-0.45900 0 CDms1 CDMSO 0.16000 0 CDms2 CDMSO 0.16000 0 [ bonds ] SDmso ODmsogb_38 SDmso CDms1gb_39 SDmso CDms2gb_39 ODmso CDms1gb_44 ODmso CDms2gb_44 CDms1 CDms2gb_45 [ angles ] ; aiajak gromos type [ impropers ] ; aiajakal gromos type [ dihedrals ] ; aiajakal gromos type *** dmso.itp file which i am using for dmso is following. [ moleculetype ] ; name nrexcl DMSO2 [ atoms ] ; nrtype resnr residu atomcgnrcharge 1 SD 1 DMSOSD 10.139 2 CD 1 DMSOCD1 10.16 3 OD 1 DMSOOD 1 -0.459 4 CD 1 DMSOCD2 10.16 [ bonds ] ; aiaj funct b0 kb 1 2 1 0.195 376560 ; kb from Methionine 1 3 1 0.153 502080 ; kb from C=O bond 1 4 1 0.195 376560 [ angles ] ; aiajak functtheta kt 3 1 2 1 106.75 460.240 3 1 4 1 106.75 460.240 2 1 4 197.40 460.240 ; kt from Methionine [ dihedrals ] ; ai aj ak al funct xi kxi 1 2 4 3 2 35.264 334.720; default params Any suggestions, hints or helps are most appreciated. Thanks in advance, With Regards anil > > Message: 1 > Date: Sat, 12 May 2007 16:59:40 +0530 (IST) > From: "Anil Kumar" <[EMAIL PROTECTED]> > Subject: [gmx-users] Error while running grompp for em (MD) in Urea To: gmx-users@gromacs.org > Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain;charset=iso-8859-1 > > Dear All, > > Can anyone help me in running simulation in explicit urea. > When i was using urea+h2o.gro and urea.itp and tried to do simulation in explicit urea. > After doing genbox, i am not able to do the grompp for energy minimization > and getting the error which is given below. > > I have added masses of all the atoms of urea in atommass.dat file, but still getting the same error. > Please help me, where does am i making the mistakes. > > processing coordinates... > Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) > Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) > Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) > Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) > Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) > Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) > Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) > Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) > Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) > Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) > Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) > Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3) > Warning: atom names in base.top and after_sol.gro don't match (OW - OW1) Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2) > (more than 20 non-matching atom names) > WARNING 3 [file "base.top", line 808]: > 6150 non-matching atom names > atom names from base.top will be used > atom names from after_sol.gro will be ignored > > double-checking input for internal consistency... > renumbering atomtypes... > converting bonded parameters... > # BONDS:
