[gmx-users] RE:Source code file: gmxfio.c, line: 784

2008-02-05 Thread vijay kumar hinge vijay
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

[gmx-users] Source code file: gmxfio.c, line: 784

2008-02-05 Thread vijay kumar hinge vijay
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

[gmx-users] Residue 'COA' not found in residue topology database

2007-12-30 Thread vijay kumar hinge vijay
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 t

[gmx-users] LINCS error

2007-09-17 Thread vijay kumar hinge vijay
73529 -- regards vijay kumar ___ 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 reque

[gmx-users] error regarding NA+ atom

2007-08-22 Thread vijay kumar hinge vijay
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

[gmx-users] wat is the way to solve this prob

2007-07-22 Thread vijay kumar
what is way to solve this prob Chain identifier '5' was used in two non-sequential blocks (residue 4, atom 4) the pdb file is for Si atoms no. of atoms 32 at differeent places ATOM 1 Si.66599000 .66599000 .66599000 ATOM 2 Si 7.30599000 .66599000 .66599000 ATOM

[gmx-users] pdb file of a crystal lattice of epoxy resin

2007-07-12 Thread vijay kumar
can any one send me a format of pdb file of epoxy resin,i want to simulate just epoxy resin crystal lattice cubic box size of 12 am and distance between each cube is 6 am using boundary temperature pdb file of epoxy resin CH2CHO (cubic structure) total of 8 lattices if possible topology file and st

[gmx-users] new to gromacs

2007-06-20 Thread vijay kumar
hi everyone I am new to gromacs software all i need to do is submit my project in 2 months first thing i am able to do is work with demos ,i did them perfectly but the thing is now i need to edit the water molecule pdb file and start a new project i.e. now i need to create a new pdb file with 20 m