[gmx-users] position restrain dynamics error
Dear Sir, I am succesfully run molecules upto energy minimization, in case of position restrain md step , i have following, could you help to overcome the A charge group moved too far between two domain decomposition steps. Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.021061, max 0.387149 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.00.0960 0.1332 0.0960 Step 2, time 0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.034712, max 0.636602 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.10.1332 0.1571 0.0960 Back Off! I just backed up step2b_n7.pdb to ./#step2b_n7.pdb.1# Back Off! I just backed up step2c_n7.pdb to ./#step2c_n7.pdb.1# Wrote pdb files with previous and current coordinates Step 3, time 0.006 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.023755, max 0.423951 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.00.1571 0.1367 0.0960 Step 4, time 0.008 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.051081, max 0.931870 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.30.1367 0.1855 0.0960 Back Off! I just backed up step4b_n7.pdb to ./#step4b_n7.pdb.1# Back Off! I just backed up step4c_n7.pdb to ./#step4c_n7.pdb.1# Wrote pdb files with previous and current coordinates Step 5, time 0.01 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.020335, max 0.372790 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 89.90.1855 0.1318 0.0960 Step 6, time 0.012 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.056021, max 1.029913 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.20.1318 0.1949 0.0960 Back Off! I just backed up step6b_n7.pdb to ./#step6b_n7.pdb.2# Back Off! I just backed up step6c_n7.pdb to ./#step6c_n7.pdb.2# Wrote pdb files with previous and current coordinates Step 7, time 0.014 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.024586, max 0.451876 (between atoms 360 and 363) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 360363 90.00.1949 0.1394 0.0960 with regards S. Boopathi -- gmx-users mailing listgmx-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] reg minimization problem
Dear sir, i have running new molecules add in standard protein that new is morin molecules unfortunetly 102 error occur which is no defualt angle found , etc. i overcome this problem but one more new appear which is shown below could you help me to overcome these following errror 26 atoms are not part of any of the T-Coupling groups can you tell what is the necessary steps carry to overcome this mistake with regards S. BOopathi -- gmx-users mailing listgmx-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] REG: grompp comment
Dear sir, i have successfully created .gro file after neccessary correction made in .rtp file. In the grompp_d comment, i am facing following errror. could how can i rectify this error. my comment is ./grompp_d -f em.mdp -c abnic2.gro -p abnic.top -o abnic2.tpr WARNING 1 [file em.mdp, line 12]: Unknown left-hand 'coloumbtype' in parameter file WARNING 2 [file em.mdp, line 12]: Unknown left-hand 'rcoloumb' in parameter file Generated 2278 of the 2278 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2278 of the 2278 1-4 parameter combinations ERROR 1 [file abnic_Other.itp, line 54]: No default Bond types ERROR 2 [file abnic_Other.itp, line 60]: No default Bond types ERROR 3 [file abnic_Other.itp, line 61]: No default Bond types ERROR 4 [file abnic_Other.itp, line 62]: No default Bond types ERROR 5 [file abnic_Other.itp, line 63]: No default Bond types ERROR 6 [file abnic_Other.itp, line 64]: No default Bond types ERROR 7 [file abnic_Other.itp, line 65]: No default Bond types ERROR 8 [file abnic_Other.itp, line 66]: No default Bond types ERROR 9 [file abnic_Other.itp, line 67]: No default Bond types ERROR 10 [file abnic_Other.itp, line 68]: No default Bond types ERROR 11 [file abnic_Other.itp, line 69]: No default Bond types ERROR 12 [file abnic_Other.itp, line 70]: No default Bond types ERROR 13 [file abnic_Other.itp, line 71]: No default Bond types ERROR 14 [file abnic_Other.itp, line 72]: No default Bond types ERROR 15 [file abnic_Other.itp, line 73]: No default Bond types ERROR 16 [file abnic_Other.itp, line 74]: No default Bond types ERROR 17 [file abnic_Other.itp, line 150]: No default Angle types ERROR 18 [file abnic_Other.itp, line 151]: No default Angle types ERROR 19 [file abnic_Other.itp, line 152]: No default Angle types ERROR 20 [file abnic_Other.itp, line 156]: No default Angle types ERROR 21 [file abnic_Other.itp, line 157]: No default Angle types ERROR 22 [file abnic_Other.itp, line 158]: No default Angle types ERROR 23 [file abnic_Other.itp, line 159]: No default Angle types ERROR 24 [file abnic_Other.itp, line 160]: No default Angle types ERROR 25 [file abnic_Other.itp, line 161]: No default Angle types ERROR 26 [file abnic_Other.itp, line 162]: No default Angle types ERROR 27 [file abnic_Other.itp, line 163]: No default Angle types ERROR 28 [file abnic_Other.itp, line 164]: No default Angle types ERROR 29 [file abnic_Other.itp, line 165]: No default Angle types ERROR 30 [file abnic_Other.itp, line 166]: No default Angle types ERROR 31 [file abnic_Other.itp, line 167]: No default Angle types ERROR 32 [file abnic_Other.itp, line 168]: No default Angle types ERROR 33 [file abnic_Other.itp, line 169]: No default Angle types ERROR 34 [file abnic_Other.itp, line 170]: No default Angle types ERROR 35 [file abnic_Other.itp, line 171]: No default Angle types ERROR 36 [file abnic_Other.itp, line 172]: No default Angle types ERROR 37 [file abnic_Other.itp, line 173]: No default Angle types ERROR 38 [file abnic_Other.itp, line 174]: No default Angle types ERROR 39 [file abnic_Other.itp, line 175]: No default Angle types ERROR 40 [file abnic_Other.itp, line 176]: No default Angle types ERROR 41 [file abnic_Other.itp, line 177]: No default Angle types ERROR 42 [file abnic_Other.itp, line 178]: No default Angle types ERROR 43 [file abnic_Other.itp, line 179]: No default Angle types ERROR 44 [file abnic_Other.itp, line 180]: No default Angle types ERROR 45 [file abnic_Other.itp, line 181]: No default Angle types ERROR 46 [file abnic_Other.itp, line 182]: No default Angle types ERROR 47 [file abnic_Other.itp, line 183]: No default Angle types ERROR 48 [file abnic_Other.itp, line 184]: No default Angle types ERROR 49 [file abnic_Other.itp, line 185]: No default Angle types ERROR 50 [file abnic_Other.itp, line 186]: No default Angle types ERROR 51 [file abnic_Other.itp, line 187]: No default Angle types ERROR 52 [file abnic_Other.itp, line 188]: No default Angle types ERROR 53 [file abnic_Other.itp, line 189]: No default Angle types ERROR 54 [file abnic_Other.itp, line 190]: No default Angle types ERROR 55 [file abnic_Other.itp, line 191]: No default Angle types ERROR 56 [file abnic_Other.itp, line 192]: No default Angle types ERROR 57 [file abnic_Other.itp, line 193]: No default Angle types ERROR 58 [file abnic_Other.itp, line 195]: No default Angle types ERROR 59 [file abnic_Other.itp, line 196]: No default Angle types ERROR 60 [file abnic_Other.itp, line 197]: No default Angle types ERROR 61 [file abnic_Other.itp, line 202]: No default Proper Dih. types ERROR 62 [file abnic_Other.itp, line 203]: No default Proper Dih. types ERROR 63 [file abnic_Other.itp, line 204]: No default Proper Dih. types ERROR
[gmx-users] REGARDING DOUBT
dear sir, i have give input that is* ./pdb2gmx_d -f activesite16-22.pdb -water tip3p -ignh* but i face some* errror like There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Edit a .n.tdb and/or .c.tdb fi*le. i have made necessary correction in the .rtp file acccording to my pdb file. with regards S.BOOPATHI -- gmx-users mailing listgmx-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] (no subject)
how to assign charge and charge group number when new residue as being added to the existing amino acid rtp file -- gmx-users mailing listgmx-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] regarding missing atom
dear sir, i was doing gromacs when i run pdb2gmmx i got following error that is some atom missing -- gmx-users mailing listgmx-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
