[gmx-users] problem with angle restraints
I trying to use angle restrain for an ligand molecule. I have included the following information in my .itp file of the ligand - [ angle_restraints ] ; aiajak functc0c1c2c3 6 1 7 1 106.9510001 6 1 8 1 108.8310001 7 1 8 1 104.9610001 5 2 7 1 110.6610001 5 2 8 1 104.9810001 When I am running the grompp command , I am getting an error- Incorrect number of parameters - found 2, expected 3 or 6 for Angle Rest.. -- I have gone through the manual it says that for angle restrains we have to provide the theta(degree);fc; multi.I have given all the relevant information but still there is error. Please tell me where I have gone wrong. Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: Subject: [gmx-users] error compiling mopac and gromacs
According to the suggestion I have installed the f2c package in my machine.I am unable to find the g2c package. I have included the f2c library by - export LIBS=-lmopac -lf2c. But when I running ./configure --with-qmmm-mopac --disable-float , an error is comming C compiler cannot create executable. The config.log file shows the following section- onfigure:3413: checking for C compiler default output file name configure:3440: cc -I/usr/local/include -DUSE_MOPAC -L/usr/local/lib conftest.c -lmopac -lf2c 5 /usr/lib/gcc/i486-linux-gnu/4.3.3/../../../../lib/libf2c.so: undefined reference to `MAIN__' collect2: ld returned 1 exit status configure:3443: $? = 1 configure:3481: result: configure: failed program was: | /* confdefs.h. */ Please suggest a way out.Subarna Thakur From: Gerrit Groenhof ggro...@gwdg.de To: gmx-users@gromacs.org Sent: Sat, 12 June, 2010 3:36:54 PM Subject: Re: Subject: [gmx-users] error compiling mopac and gromacs Depending on how your libmopac.a was biuld, you need the to include the f2c or g2c library as well. Gerrit Message: 5 Date: Sat, 12 Jun 2010 14:33:02 +0530 (IST) From: subarna thakur thakur.suba...@yahoo.co.in Subject: [gmx-users] error compiling mopac and gromacs To: gmx-users@gromacs.org Message-ID: 371899.78968...@web95516.mail.in.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hi I am trying to link mopac with gromacs in a 32 bit linux machine. I have downloaded the libmopac.a file and kept it under /usr/local/lib. I installed fftw with double precision and then I set the enviornmental variables for linking mopac and gromacs export LDFLAGS=-L/usr/local/lib -Wl,--wrap,__ctype_b export CPPFLAGS=/usr/local/include -DUSE_MOPAC export LIBS=lmopac then I have ran the ./configure --with-qmmm-mopac --disable-float.It seems to run ok.Then I used the make command but an error is comming as follows- /usr/local/lib/libmopac.a(lread.o)(.text+0x160): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x21f): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x296): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x2d0): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x8b2): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0xb05): more undefined references to `__wrap___ctype_b' follow collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/usr/gromacs-4.0.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/usr/gromacs-4.0.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/usr/gromacs-4.0.3/src' make: *** [all-recursive] Error 1 Please suggest where I have gone wrong. Subarna Thakur -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20100612/ed0e12b1/attachment.html -- -- 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/search before posting! End of gmx-users Digest, Vol 74, Issue 69 * -- Gerrit Groenhof MPI biophysical chemistry Goettingen Germany http://wwwuser.gwdg.de/~ggroenh/ -- 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/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] error in linking mopac and gromacs
According to the suggestion I have installed the f2c package in my machine.I am unable to find the g2c package. I have included the f2c library by - export LIBS=-lmopac -lf2c. But when I running ./configure --with-qmmm-mopac --disable-float , an error is comming C compiler cannot create executable. The config.log file shows the following section- onfigure:3413: checking for C compiler default output file name configure:3440: cc -I/usr/local/include -DUSE_MOPAC -L/usr/local/lib conftest.c -lmopac -lf2c 5 /usr/lib/gcc/i486-linux-gnu/4.3.3/../../../../lib/libf2c.so: undefined reference to `MAIN__' collect2: ld returned 1 exit status configure:3443: $? = 1 configure:3481: result: configure: failed program was: | /* confdefs.h. */ Please suggest a way out.Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] error compiling mopac and gromacs
Hi I am trying to link mopac with gromacs in a 32 bit linux machine. I have downloaded the libmopac.a file and kept it under /usr/local/lib. I installed fftw with double precision and then I set the enviornmental variables for linking mopac and gromacs export LDFLAGS=-L/usr/local/lib -Wl,--wrap,__ctype_b export CPPFLAGS=/usr/local/include -DUSE_MOPAC export LIBS=lmopac then I have ran the ./configure --with-qmmm-mopac --disable-float.It seems to run ok.Then I used the make command but an error is comming as follows- /usr/local/lib/libmopac.a(lread.o)(.text+0x160): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x21f): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x296): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x2d0): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0x8b2): In function `e_rsle': : undefined reference to `__wrap___ctype_b' /usr/local/lib/libmopac.a(lread.o)(.text+0xb05): more undefined references to `__wrap___ctype_b' follow collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/usr/gromacs-4.0.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/usr/gromacs-4.0.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/usr/gromacs-4.0.3/src' make: *** [all-recursive] Error 1 Please suggest where I have gone wrong. Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] angle restraints
hello I want to add angle restraints in my itp file for a ligand. what is the proper way of inserting angle restraint in .itp file ? Is there any keywords I have to add to my .mdp file for angle restraints? I have searched the mail archieve, I found many things about adding dihedral angle restraints but I couldnot find anything about adding angle restrains. Please advice. Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] shake and settle
Hi gmx user I want to use shake algorithm for bonds within protein and settle algorithm for the bonds of the water. How do I specify two different constraints algorithm in pr.mdp file? Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] adding constraints
Hi all, I want to add constraints for bond length of a ligand.Where do I place the constraints statement in the .rtp file or in the .top file? Subarna Thakur -- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] linc warnings
Hi My protein has a Fe4S4 cluster. I have been able to minimize the structure using Steepest descent. The log file shows following message: Steepest Descents converged to Fmax 2000 in 372 steps Potential Energy = -4.1580605e+06 Maximum force = 1.7402682e+03 on atom 820 Norm of force = 3.0794989e+01 - But during the position restraining step, following Linc warning is coming before stopping all-together Step 228, time 0.456 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 51159085.131913, max 1100381184.00 (between atoms 5437 and 5444) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1262 1264 38.80.1009 0.1054 0.1000 1262 1263 83.60.1035 0.0960 0.1000 1261 1265 42.10.1349 0.1366 0.1340 1259 1261 42.90.1359 0.1372 0.1340 1237 1241 33.00.1480 0.1788 0.1470 1235 1237 75.60.1360 0.4797 0.1330 1235 1236 40.90.1254 0.3422 0.1230 1232 1233 71.30.1834 0.3421 0.1830 1231 1232 43.10.1559 0.3294 0.1530 1230 1235 106.00.1589 0.2070 0.1530 1230 1231 111.00.1606 0.3819 0.1530 1228 1230 81.90.1535 8.3688 0.1470 1228 1229 100.80.1040 7.2523 0.1000 1226 1228 108.70.1480 29.6051 0.1330 1226 1227 112.00.1271 25.3002 0.1230 1224 1226 67.70.2210 50.5775 0.1530 1224 1225 73.60.2217 43.8606 0.1530 1222 1224 146.53.0118 273.3403 0.1470 1222 1223 173.15.0766 350.6593 0.1000 1220 1222 140.6 50.1464 1239.3472 0.1330 1220 1221 142.5 50.5481 1210.8007 0.1230 1218 1219 46.50.1089 0.0687 0.1090 1216 1218 106.30.1532 2.4558 0.1390 1216 1217 57.30.1434 2.4980 0.1090 1214 1218 106.40.1028 2.6673 0.1390 1214 1215 166.40.2538 2.1798 0.1090 1212 1216 119.00.5844 15.3761 0.1390 1212 1213 50.70.5406 17..8588 0.1090 1210 1214 116.20.9490 16.1642 0.1390 1210 1211 150.40.7387 23.8303 0.1090 1209 1212 57.44.3532 165.6521 0.1390 1209 1210 53.54.3615 166.9433 0.1390 1208 1209 130.9 34.7441 858.7278 0.1530 1207 1220 174.9 199.1050 3552.6362 0.1530 1207 1208 172.1 195.9491 3367.8894 0.1530 1205 1207 176.1 490.9904 5776.2954 0.1470 1205 1206 177.8 631.7326 5326.1118 0.1000 1203 1205 179.0 1242.0747 9168.7764 0.1330 1203 1204 178.9 1057.3107 7388.7915 0.1230 1202 1203 179.3 1221.3862 8532.1836 0.1530 1200 1202 177.8 455.7037 3702.9392 0.1470 1200 1201 172.7 158.7020 1978.1310 0.1000 1198 1200 174.2 160.3432 1536.1411 0.1330 1198 1199 92.0 16.9060 423.7516 0.1230 1197 1198 94.1 16.9010 421.8028 0.1530 1195 1197 99.1 10.3514 9.3388 0.1470 1195 1196 96.29.0920 8.6023 0.1000 1193 1195 91.2 21.5753 58.1620 0..1330 1193 1194 89.2 21.1892 62.7649 0.1230 1191 1192 90.1 50.3829 12.4455 0.1330 1190 1191 89.4 13.1419 10.9133 0.1830 1189 1193 114.3 75.7546 37.4387 0.1530 1189 1190 91.1 24.9488 56.3341 0.1530 1187 1189 146.9 53.8226 42.4679 0.1470 1187 1188 139.0 22.0031 100.4932 0.1000 1185 1187 163.3 21.1472 184.6258 0.1330 1185 1186 170.3 61.0351 169.5860 0.1230 1182 1184 153.34.0050 30.0847 0.1530 1182 1183 109.92.7482 31.3314 0.1530 1181 1185 170.1 69.8200 192.5774 0.1530 1181 1182 129.0 21.4261 109.4787 0.1530 1179 1181 132.8 19.8073 116.5793 0.1470 1179 1180 159.42.3810 48.3401 0..1000 1177 1179 175.21.4786 53.0837 0.1330 1177 1178 166.40.7559 28.5291 0.1230 1174 1176 90.00.1801 80.6845 0.1530 1174 1175 99.70.2091 19.2129 0.1530 1173 1177 149.10.2721 28.0611 0.1530 1173 1174 73.60.7968 36.5323 0.1530 1171 1173 87.80.8744 115.1496 0.1470 1171 1172 91.20.1603 111.8982 0.1000 1169 1171 89.70.2456 106.5120 0.1330 1169 1170 90.00.1499 17.6986 0.1230 1166 1168 76.10.1256 0.4912 0.1250 1166 1167 77.80.1256 0.4782 0.1250 1165 1166 71.90.1546 2.7698 0.1530 1164 1169 83.50.1781 17.7449 0.1530 1164 1165 89.30.1594 8.0829 0..1530 1162 1164 88.00.1531 8.2075 0.1470 1162 1163 75.00.1015 0.7203 0.1000 1160 1162 77.50.1343 1.0789
Re: [gmx-users] linc warnings
Hi, I am using the following keywords in pr.mdp file for the simulation for protein with fe4s4 cluster; title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 150; total 3000 ps. nstcomm = 1 nstxout = 500 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps= ProteinNon-Protein tau_t = 0.10.1 ref_t = 300300 ; Energy monitoring energygrps= Protein Non-Protein ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 But the Fe4s4 cluster atoms are showing large rms and rotating hugely in position restraining step and Linc warnings are comming. In some published papers it is mentioned that during the molecular dynamics simulations, the proteins' heavy atoms and the counter ions were harmonically restrained to their initial positions of pdb, How can I do this for my fe4s4 cluster. What keywords should I use for that and in which step I can do? subarna From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tue, 29 December, 2009 5:44:03 PM Subject: Re: [gmx-users] linc warnings subarna thakur wrote: Hi My protein has a Fe4S4 cluster. I have been able to minimize the structure using Steepest descent. The log file shows following message: Steepest Descents converged to Fmax 2000 in 372 steps Potential Energy = -4.1580605e+06 Maximum force = 1.7402682e+03 on atom 820 Norm of force = 3.0794989e+01 - But during the position restraining step, following Linc warning is coming before stopping all-together If EM worked nicely, then something else you are doing is incorrect. snip the atoms 5437,5438,5439 are the FE atoms of the Fe4S4 cluster. these atoms are rotating hugely and showing large rms. Please suggest how to tackle the FE atoms during simulation run ? Without the metal cluster, the same protein is working fine under simulation and there is no such linc warinings? Without seeing your .mdp file and perhaps even snippets of your topology pertaining to the Fe4S4 cluster, there's nothing else to say except please read the standard advice: http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings -Justin Subarna The INTERNET now has a personality. YOURS! See your Yahoo! Homepage http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/. -- 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 listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] freeze group
I running the simulation of a protein with Fe4s4 cluster. The parameters for the cluster were obtained from a previously published paper. I have been able to carry out energy minimization with the following keywords- ; cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 2000 ; ; Energy minimizing stuff ; emtol = 2000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no -- The output showsSteepest Descents converged to Fmax 2000 in 203 steps Potential Energy = -5.8639745e+06 Maximum force = 1.7305787e+03 on atom 777 Norm of force = 4.4084099e+01 But when I am trying the position retraining step, with following keywords in pr.mdp file- title = Yo cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 1 ; total 20.0 ps. nstcomm = 1 nstxout = 250 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.4 ; Berendsen temperature coupling is on Tcoupl = v-rescale tc-grps = Protein SOL SF4 tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 ; Energy monitoring energygrps = Protein SOL SF4 ; Pressure coupling is on Pcoupl = parrinello-rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 an error is generated with LINCS warningStep 155, time 0.31 (ps) LINCS WARNING relative constraint deviation after LINCS: rms inf, max 14002532367890120704.00 (between atoms 5093 and 5096) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1193 1195 40.1 0.1330 0.1913 0.1330 1193 1194 38.7 0.1230 0.1757 0.1230 1191 1192 77.7 0.1530 210.9258 0.1530 1189 1193 63.7 0.1530 193.1889 0.1530 1189 1190 75.9 0.1530 193.1568 0.1530 1188 1192 65.6 0.1470 893.4214 0.1470 1188 1189 67.7 0.1470 909.7200 0.1470 1186 1188 72.8 0.1330 3701.8413 0.1330 1186 1187 78.6 0.1230 3824.8157 0.1230 1184 1185 79.5 0.1780 57.6559 0.1780 1183 1184 79.3 0.1829 539.6799 0.1830 1182 1183 85.5 0.1530 3695.6021 0.1530 1181 1186 84.6 0.1530 14910.0859 0.1530 1181 1182 86.6 0.1530 15403.3672 0.1530 1179 1181 87.4 0.1470 35502.0234 0.1470 1179 1180 89.9 0.1000 1119163.2500 0.1000 1177 1179 86.7 0.1330 37732.0156 0.1330 1177 1178 85.9 0.1230 17608.4004 0.1230 1175 1177 99.6 0.1530 50041.0938 0.1530 1175 1176 102.3 0.1530 37907.5586 0.1530 1173 1175 117.7 0.1470 698413.0625 0.1470 1173 1174 120.6 0.1000 677364.4375 0.1000 1171 1173 107.2 0.1330 4168765.5000 0.1330 1171 1172 108.5 0.1230 4103918.2500 0.1230 1169 1170 112.9 0.1090 9872814. 0.1090 1167 1169 92.1 0.1390 68041384. 0.1390t = 0.310 ps: Water molecule starting at atom 196197 can not be settled. Check for bad contacts and/or reduce the timestep. Wrote pdb files with previous and current coordinates - These atoms 5093 and 5096 are the Iron atoms of the cluster. Now My question is- a) Can I freeze the movement of the Fe4S4 cluster during simulation by incorporating the cluster in freeze group? b) If yes, then how do I incorporate the freeze group in Pr.mdp file during position restraining step? c) Is there any other alternative to correct the linc warning error? The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy minimization
Hello Can increase the emtol from 1000 to 1 KJ mol - 1 nm-1? subarna From: Mark Abraham mark.abra...@anu.edu.au To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thu, 10 December, 2009 2:33:23 PM Subject: Re: [gmx-users] energy minimization subarna thakur wrote: I am doing the energy minimization of a protein using the following keywords in em.mdp file- cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 3000 ; ; Energy minimizing stuff ; emtol = 1000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no - I am getting the ouput as following- Steepest Descents converged to machine precision in 67 steps, but did not reach the requested Fmax 1000. Potential Energy = -4.0967048e+06 Maximum force = 3.7720719e+04 on atom 5530 Norm of force = 1.7014005e+02 - Can anybody suggest what changes I can make Well you can play with the EM step size, or see if atom 5530 looks unhappy, or you can move on to your equilibration and hope nothing's seriously wrong. Mark -- 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/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/mailing_lists/users.php The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy minimization
I am doing the energy minimization of a protein using the following keywords in em.mdp file- cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 3000 ; ;Energy minimizing stuff ; emtol = 1000 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 coulombtype = PME rcoulomb= 1.0 rvdw= 1.0 Tcoupl = no Pcoupl = no gen_vel = no - I am getting the ouput as following- Steepest Descents converged to machine precision in 67 steps, but did not reach the requested Fmax 1000. Potential Energy = -4.0967048e+06 Maximum force = 3.7720719e+04 on atom 5530 Norm of force = 1.7014005e+02 - Can anybody suggest what changes I can make The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] query regarding itp file
Hi Can any body please tell me what does c0 and c1 column represent in .itp file? And how do I obtain these parameters for a ligand. Subarna thakur The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] topology file in .dat format
Hello I have a gromos96 topology file for a ligand and it is in xx.dat format.How do I include this file in my gromacs version 4.0 simulation of a protein? Subarna The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/-- gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] rmsf
Hello I want to analyze the RMSF fluctuation of each residue of a protein during a simulation run. I am giving the command g_rmsf -f md.xtc -s md.tpr -b 4000 -e 6000 -o traj_rmsf.xvg -ox traj_avg.pdb. Then I am selecting the whole protein for the analysis. I am getting the RMSF per atom in the .xvg file and I have to plot the graph as RMSF versus atom no. but I want to have the RMSF of each amino acid residue.How Can I get the RMSF of each residue , what is the command for that? Subarna Connect more, do more and share more with Yahoo! India Mail. Learn more. http://in.overview.mail.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] dssp programm
Hello I installed the dssp program for obtaining the secondary structure.I used the dssp programm to analyze the secondary structure of the protein after a MD simulation run. I got the out of the pogramm as m.dssp but I want to know how do I represent the output of the dssp programm graphically or how do I visualize the output of the dssp programm. regards subarna Yahoo! India has a new look. Take a sneak peek http://in.yahoo.com/trynew___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] query regarding ffG43a1bon.itp
Hello I want to add a new bond streching parameter in the ffG43a1bon.itp file, Can anybody please tell me how the values under Examples of usage in terms of non-bonded atom types'' determined of each bond in the file ffG43a1bon.itp Subarna Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] desciption of ffG43a1bon.itp
Hello In the file ffG43a1bon.itp, the bond parameters are given like this- -- ICB(H)[N] CB[N] B0[N] ; #define gb_1 0. 1000 1.5700e+07 ; H - OA 750 ; #define gb_2 0. 1000 1.8700e+07 ; H - N (all) 895 ; #define gb_3 0. 1090 1.2300e+07 ; HC - C 700 Can anybody please tell me, which one is is the force constant and which one is ideal bond length. For describing a new bond parameters , what the values I have to provide in the file ffG43a1bon.itp. The ffG43a1bon.itp is not clearly described in the chapter5 of the manual of gromacs version4. Subarna Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] parameterization of ligand
Hello I have received a parameter of a ligand of a protein from the author of an earlier published work.The parameter is in param.dat format based on ff43a1 force field. Can anybody plz suggest how and where do I put the parameter file in the gromacs.I am using gromacs 4.0 version. Regards Subarna Looking for local information? Find it on Yahoo! Local http://in.local.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] FeS cluster
Hello We dont have the parameters for Fe4S4 cluster in any of the the gomacs force fields but if we able to make the .itp file for the cluster manually with the help of Quantum mechanical calculations, can we place the .itp file of fe4s4 in the include section of the protein .top file later as done in the case of drug/enzyme tutorial of gromacs.Can we fellow the steps given in the tutorial for the Fe4S4 cluster? With regards Subarna Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fes cluster
Hello The protein I am considering is a homodimer with two chains with a Fe4S4 cluster situated at the interface of two chains with connections with both the chains by cystein residues.I have generated the .itp file of the Fe4S4 cluster and .top of the protein with pdb2gmx command.The .top file is like this- -; ; File '1braf.top' was generated ; By user: root (0) ; On host: localhost.localdomain ; At date: Mon Jul 27 13:12:40 2009 ; ; This is your topology file ; I Have a Bad Case Of Purple Diarrhea (Urban Dance Squad) ; ; Include forcefield parameters #include ffoplsaa.itp ; Include chain topologies #include 1braf_A.itp #include 1braf_B.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_A 1 Protein_B 1 - I want to know how do I include the Fe4S4 .itp file in the topology file of the protein and How do I include the connect information of the protein and FES cluster. Regards Subarna Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with topolbuild execution
Hello I am trying to generate a .itp file of a Fe4S4 cluster from mol2 file with the help of topolbuild1_2_1 programm but a error is comming during execution stating Illegal characters for size information line. I dont know what is wrong with the input file. I am giving here the input mol2 file I am using- -- @TRIPOSMOLECULE SF4_ideal.pdb 8 12 0 0 0 SMALL GASTEIGER Energy = 0 @TRIPOSATOM 1 FE1 -0.1560 1.1840 1.4740 Fe 1 SF41 0.2771 2 FE2 1.4550 -1.1820 0.2890 Fe 1 SF41 0.2779 3 FE3 0.3020 0.9990 -1.5840 Fe 1 SF41 0.2526 4 FE4 -1.6010 -1.0010 -0.1800 Fe 1 SF41 0.2284 5 S1 0.1560 -1.1840 -1.4740 S.3 1 SF41 0.2379 6 S2 -1.4550 1.1820 -0.2890 S.3 1 SF41 0.2356 7 S3 -0.3020 -0.9990 1.5840 S.3 1 SF41 0.2487 8 S4 1.6010 1.0010 0.1800 S.3 1 SF41 0.2414 @TRIPOSBOND 1 1 6 1 2 1 7 1 3 1 8 1 4 2 5 1 5 2 7 1 6 2 8 1 7 3 5 1 8 3 6 1 9 3 8 1 10 4 5 1 11 4 6 1 12 4 7 1 @TRIPOS --- Please suggest the changes I should make in the input file to execute the topolbuild programm Regards Subarna Thkaur Looking for local information? Find it on Yahoo! Local http://in.local.yahoo.com/ sf4.mol2 Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] query regarding Fe4S4
Hello I have generated the individual charges of Fe4S4 cluster with Gaussian programm.I have all the interatomic distances and diherdral.I ahve also generated the .top file of the Fe4S4 cluster with the help of mktop pogramm.Can anybody please suggest how do I generated the .itp file for the Fe4S4 cluster.Do I have to do it manually? Isnt there any other way? Subarna Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] query about topolgen.pl
Hi Can any body please tell me how to install and execute topolgen.pl script in linux for generationf topology file. It is not given in the Readme file. Subarna Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] query regarding .top file
Hello I have generated .top file for an ligand with the mktop programm for OPLSAA force field , how do I include this .top file for the ligand along with that my protein in the gromacs run? Subarna Looking for local information? Find it on Yahoo! Local http://in.local.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with installation of topolbuild1.2.1
Hi Can anybody please tell me how to install topolbuild 1.2.1 programm in 32 bit machine with Fedora linux operating system. I cannot understand the instruction given in the READ ME file Subarna See the Web#39;s breaking stories, chosen by people like you. Check out Yahoo! Buzz. http://in.buzz.yahoo.com/___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] choosing force filed
Hello Can any body please suggest which force field would be appropiate for simulation of protein with Fe-S cluster? Can I use the opls-aa force field for such simulations? Subarna Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] parameters of Fe-S cluster
Hello Does anyone have the topology parameters for Fe-S cluster ? Subarna ICC World Twenty20 England #39;09 exclusively on YAHOO! CRICKET http://cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem of getting with Dssp
Hi I want to install dssp programm in my linux machine but I am not getting it from the website http://swift.cmbi.ru.nl/gv/dssp/. The linux executable given in the website does not seems to work.Can any one suggest any alternative site for downloading the current version of dssp. Subarna Cricket on your mind? Visit the ultimate cricket website. Enter http://cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Problem wih Fe-S cluster
Hi everyone I am facing a problem with derivation of parameters of Fe-S cluster in a protein.Can anybody please tell me for deriving a parameters do I have to consider the co-ordinates of a typical fe-s cluster as there in Protein Data Base (PDB) or the co-ordinates of the Fe-S cluster present in my protein of interest. Subarna Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.yahoo.com___ gmx-users mailing listgmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] gromos type in .rtp file
hello everyone Can any body please explain to me, what does the trm gb_38 or gb_39 stand for under the bond coulmn of the .rtp file ? what is gromos type under angles and impropers? Subarna Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in..travel.yahoo.com/___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with FeS cluster
Hello user Can anybody please tell me how to prepare a topology file for the FES4 cluster incorporated in a protein Subarna Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with FeS cluster
Hi I have gone through the material you have earlier mentioned but I am still in dark and not sure where to start. Should I make chages in the relevent .rtp file to incorporate the atoms of the FE-S cluster? Subarna From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-us...@gromacs..org Sent: Wednesday, 3 June, 2009 4:46:37 PM Subject: Re: [gmx-users] problem with FeS cluster subarna thakur wrote: Hello user Can anybody please tell me how to prepare a topology file for the FES4 cluster incorporated in a protein I passed along some useful information to you yesterday. There is no easy answer. To do so would involve a large amount of work, in any case, if it is even possible to model this species using a standard MM force field. -Justin Subarna Cricket on your mind? Visit the ultimate cricket website. Enter now! http://in.rd.yahoo.com/tagline_cricket_1/*http://beta.cricket.yahoo..com ___ gmx-users mailing list gmx-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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Own a website.Get an unlimited package.Pay next to nothing.*Go to http://in.business.yahoo.com/___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with generation of .gro file
Hello, I am running the pdb2gmx command for a homodimer protein with SF4 (a ferro-sulphur cluster) ligand but it fails to generate the .gro file. A error is coming SF4 not found in residue topology database. I have trired all the different force fields. Can anybody please tell me how to correct the error? How to modify the rtp file to consider the ligand? Subarna thakur University of north bengal Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo..com___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
