Dear Justin Thank you for your previous reply When i run the .pdb2gmx_d -f 1OG2O.pdb -o 1OG2O.gro -p 1OG2O.top -renum It runs successfully. But i have on issue. My PDB contains HIS residues in both chain A and B I have selected
GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) The .rtp file of this force field does not contain any [ HIS ] residue so it takes HIS as HISE as shown in the cmd prompt will ti leads to any poor construction of topology and .gro files ? . How to solve this error? Analysing hydrogen-bonding network for automated assigment of histidine protonation. 682 donors and 670 acceptors were found. There are 849 hydrogen bonds Will use HISE for residue 78 Will use HISE for residue 184 Will use HISE for residue 230 Will use HISE for residue 251 Will use HISE for residue 276 Will use HISE for residue 316 Will use HISE for residue 344 Will use HISE for residue 353 Will use HISD for residue 368 Will use HISE for residue 396 Will use HISE for residue 410 Will use HISE for residue 411 Will use HISE for residue 411 Identified residue PRO30 as a starting terminus. Identified residue HIS411 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Processing chain 2 'B' (3702 atoms, 462 residues) Analysing hydrogen-bonding network for automated assigment of histidine protonation. 682 donors and 670 acceptors were found. There are 830 hydrogen bonds Will use HISE for residue 78 Will use HISE for residue 184 Will use HISE for residue 230 Will use HISE for residue 251 Will use HISE for residue 276 Will use HISE for residue 316 Will use HISE for residue 344 Will use HISE for residue 353 Will use HISD for residue 368 Will use HISE for residue 396 Will use HISE for residue 410 Will use HISE for residue 411 Will use HISE for residue 411 Identified residue PRO30 as a starting terminus. Identified residue HIS411 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Thanks in Advance With Regards S.Vidhyasankar -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
