[gmx-users] RE:Source code file: gmxfio.c, line: 784
hiii thank for your reply mark sory for pasting other url iam using gromacs 3.3 version on sunsolaris platform,my protein contain 86 aminoacid and iam trying to unfold it at 640k hear iam pasting the command which i was used for final mdrun grompp -c 1HB6M_pr.gro -p 1HB6M.top -o 1HB6uf_b4full.tpr -f full.mdp mdrun -v -s 1HB6uf_b4full.tpr -o 1HB6uf_full.trr -c 1HB6uf_full.gro -e 1HB6uf_full.edr -g 1HB6uf_full.log -nice 0 iam trying to simulate for 300ps (15 steps),but it terminated after running step 22790(after1 hour) - the replay which i have seen in users archieve >* Hi all, *>* *>* a short simulated-annealing simulation crashes with: *>* *>* Program mdrun, VERSION 3.3.2 *>* Source code file: gmxfio.c, line: 784 *>* *>* Fatal error: *>* Can not read/write topologies to file type trr* * *>* I read the a bit the sourcecode of and it seems as if it does sth like *>* determining and setting the do_read/write functions for file I/O. *>* *>* Any idea where this could come from? * try a clean compile (make distclean; configure and so on). >* *>* Best *>* Martin regards vijay * ___ 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] Source code file: gmxfio.c, line: 784
Hi all, iam trying to unfold 86 amino acid contain peptide at 640k . but my final mdrun terminated with following error: - 15 steps,300.0 ps. step 22790, will finish at Tue Feb 5 19:41:24 2008- Program mdrun, VERSION 3.3 Source code file: gmxfio.c, line: 784 Fatal error: Can not read/write topologies to file type trr --- i got one hit regarding my query from archive which iam not able to resolve.hear iam attaching the link http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ i would like to know how can i solve the problem thank you in advance - VIJAY ___ 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] Residue 'COA' not found in residue topology database
Hello users, iam using gromacs 3.3 version on linux platform.my protein contain 86 residues and ligand molecule (palmityl coA) i got the error while running pdb2gmx with force field gromacs96 43a1.it is saying that Fatal error: Residue 'COA' not found in residue topology database i wil be very thank full to you if any one can give the sugesstion -- HINGE VIJAYA KUMAR SUN-CoE in Medical Bioinformatics EMBnet INDIA node Centre for DNA Fingerprinting and Diagnostics (CDFD), Gundipet, Hyderabad INDIA-500 076 Ph.No : +91-40-27151344 ___ 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] LINCS error
hello users, i am using gromacs 3.3 version on unix platform i got these error while running MD simulation of 89 aa in spc216 water for 10ns at step 4088373 time 8176.55 .i had used force field 4a1(official distribution) hear I'm sending .mdp file also error which i got is -- step 4088520, will finish at Sat Sep 22 06:22:35 2007 Step 4088530, time 8177.06 (ps) LINCS WARNING relative constraint deviation after LINCS: max 17.051964 (between atoms 615 and 616) rms 0.709711 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 613614 35.70.1233 0.1232 0.1230 613615 35.20.1332 0.1352 0.1330 615616 90.00.0997 1.8052 0.1000 615617 90.00.1322 1.3965 0.1000 step 4088530, will finish at Sat Sep 22 06:22:35 2007Warning: 1-4 interaction at distance larger than 1 These are ignored for the rest of the simulation turn on -debug for more information Step 4088531, time 8177.06 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1.625723 (between atoms 615 and 617) rms 0.062578 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 612613 46.40.1548 0.1344 0.1530 613614 37.20.1232 0.1816 0.1230 613615 89.70.1352 0.2216 0.1330 615616 76.31.8052 0.1476 0.1000 615617 89.71.3965 0.2626 0.1000 Step 4088532, time 8177.06 (ps) LINCS WARNING relative constraint deviation after LINCS: max 14.399930 (between atoms 615 and 616) rms 0.598937 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 611612 44.20.1693 0.1761 0.1530 612613 35.40.1344 0.1669 0.1530 613614 95.70.1816 0.1308 0.1230 615616 90.20.1476 1.5400 0.1000 615617 90.50.2626 1.1927 0.1000 Step 4088533, time 8177.07 (ps) LINCS WARNING relative constraint deviation after LINCS: max 1.051080 (between atoms 615 and 617) rms 0.046065 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 609611 44.50.1529 0.1910 0.1470 611612 39.90.1761 0.1800 0.1530 611618 41.90.1579 0.1736 0.1530 612613 105.90.1669 0.2124 0.1530 613614 123.80.1308 0.1181 0.1230 613615 34.60.1178 0.2224 0.1330 615616 74.01.5400 0.1253 0.1000 615617 80.31.1927 0.2051 0.1000 Step 4088534, time 8177.07 (ps) LINCS WARNING relative constraint deviation after LINCS: max 45040.144531 (between atoms 613 and 614) rms 1994.670654 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 582584 41.90.1470 0.2116 0.1470 584585 41.30.1530 0.2102 0.1530 584586 69.20.1530 8.3830 0.1530 586587 59.20.1230 8.3382 0.1230 586588 78.90.1331 28.5889 0.1330 588589 75.70.1001 27.4635 0.1000 588590 80.70.1471 156.4029 0.1470 590591 82.50.1531 156.2125 0.1530 590607 84.10.1537 272.5951 0.1530 591592 78.30.1531 23.8232 0.1530 592593 55.20.1330 6.7518 0.1330 592595 55.70.1390 6.7401 0.1390 593594 41.60.1090 0.1595 0.1090 593596 45.10.1330 0.1971 0.1330 595598 37.70.1390 0.1911 0.1390 595599 34.40.1390 0.1923 0.1390 607608 85.10.1235 322.3230 0.1230 607609 90.80.1334 722.2238 0.1330 609610 87.50.1001 730.5731 0.1000 609611 91.70.1910 2220.5916 0.1470 611612 113.10.1800 1928.0201 0.1530 611618 61.90.1736 2612.3730 0.1530 612613 152.60.2124 2170.9067 0.1530 613614 95.00.1181 5540.0610 0.1230 613615 100.80.2224 1264.8948 0.1330 615616 88.00.1253 729.0342 0.1000 615617 69.10.2051 610.1647 0.1000 618619 96.00.1365 1772.1053 0.1230 618620 101.80.1456 1954.0292 0.1330 620621 97.10.1014 161.6277 0.1000 620622 44.00.1484 387.2649 0.1470 622623 119.20.1536 271.5126 0.1530 622628 110.20.1536 303.3078 0.1530 623624 65.60.1531 51.2406 0.1530 624625 113.70.1530 26.6845 0.1530 625626 32.70.1250 0.1557 0.1250 625627 34.20.1250 0.1577
[gmx-users] error regarding NA+ atom
Respected sir/madem, i am using gromacs - 3.1.4 version on sunsolaris platform.i got error at position restrain at grompp step ,telling dat NO SUCH MOLECULE TYPE NA+(both are in caps).beofre dat the error which i got , ihv done following steps 1.first i hv excuted pdb2gmx command den i noted down the charge which given as out put.charge is -1 2.after editconf(-d 0.9),genbox ,energy minimization(grompp,mdrun) i had manipulated da .top file by adding #include 'ions.itp,removed one water molecloe from SOL and added NA+ 1 at da end of topology file . den i got error after runing da grompp of position restrain ,and i had changed pr.mdp file ,in that i was added da SOL,0.1,300 (temp) thanking u for ur patiency regards vijaya kumar hinge ___ 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
