Hi There, For the error I mentioned in last mail I looked in the .rtp file and .pdb file for residue NDP. Following is the part of .pdb file showing atoms as PA, O1A etc
HETATM 8111 PA NDP 1 8.809 -4.754 22.676 1.00 12.71 HETATM 8112 O1A NDP 1 10.106 -4.137 23.158 1.00 11.98 HETATM 8113 O2A NDP 1 8.869 -5.751 21.580 1.00 13.09 HETATM 8114 O5B NDP 1 8.010 -5.348 23.937 1.00 12.91 HETATM 8115 C5B NDP 1 6.913 -6.239 23.752 1.00 12.91 HETATM 8116 C4B NDP 1 6.493 -6.754 25.120 1.00 10.44 HETATM 8117 O4B NDP 1 5.292 -7.535 24.969 1.00 13.02 HETATM 8118 C3B NDP 1 7.588 -7.667 25.612 1.00 10.90 HETATM 8119 O3B NDP 1 7.552 -7.543 27.047 1.00 12.99 HETATM 8120 C2B NDP 1 7.086 -9.053 25.407 1.00 12.38 HETATM 8121 O2B NDP 1 7.660 -10.046 26.246 1.00 13.11 HETATM 8122 C1B NDP 1 5.579 -8.877 25.356 1.00 12.53 HETATM 8123 N9A NDP 1 4.817 -9.905 24.673 1.00 11.65 HETATM 8124 C8A NDP 1 5.033 -10.388 23.429 1.00 10.38 HETATM 8125 N7A NDP 1 4.132 -11.360 23.119 1.00 11.50 HETATM 8126 C5A NDP 1 3.332 -11.498 24.179 1.00 10.26 HETATM 8127 C6A NDP 1 2.217 -12.337 24.568 1.00 11.19 HETATM 8128 N6A NDP 1 1.746 -13.251 23.689 1.00 12.10 HETATM 8129 N1A NDP 1 1.678 -12.169 25.805 1.00 11.24 HETATM 8130 C2A NDP 1 2.130 -11.262 26.690 1.00 10.83 HETATM 8131 N3A NDP 1 3.161 -10.439 26.428 1.00 10.06 HETATM 8132 C4A NDP 1 3.776 -10.558 25.154 1.00 11.15 HETATM 8133 O3 NDP 1 7.769 -3.631 22.173 1.00 12.62 HETATM 8134 PN NDP 1 7.989 -2.036 22.130 1.00 12.08 HETATM 8135 O1N NDP 1 8.430 -1.526 23.461 1.00 11.89 HETATM 8136 O2N NDP 1 8.741 -1.692 20.889 1.00 11.73 HETATM 8137 O5D NDP 1 6.467 -1.533 21.886 1.00 12.66 HETATM 8138 C5D NDP 1 5.611 -1.361 23.020 1.00 11.65 HETATM 8139 C4D NDP 1 4.298 -0.748 22.582 1.00 11.67 HETATM 8140 O4D NDP 1 4.556 0.487 21.875 1.00 12.21 HETATM 8141 C3D NDP 1 3.548 -1.649 21.637 1.00 11.97 HETATM 8142 O3D NDP 1 2.175 -1.497 22.010 1.00 11.22 HETATM 8143 C2D NDP 1 3.579 -0.984 20.290 1.00 12.02 HETATM 8144 O2D NDP 1 2.475 -1.229 19.433 1.00 11.31 HETATM 8145 C1D NDP 1 3.974 0.454 20.593 1.00 12.46 HETATM 8146 N1N NDP 1 4.714 1.092 19.529 1.00 11.43 HETATM 8147 C2N NDP 1 6.045 0.998 19.502 1.00 11.26 HETATM 8148 C3N NDP 1 6.724 1.599 18.453 1.00 10.05 HETATM 8149 C7N NDP 1 8.217 1.540 18.362 1.00 11.67 HETATM 8150 O7N NDP 1 8.756 2.105 17.403 1.00 11.17 HETATM 8151 N7N NDP 1 8.916 0.848 19.266 1.00 11.33 HETATM 8152 C4N NDP 1 6.022 2.270 17.471 1.00 10.99 HETATM 8153 C5N NDP 1 4.641 2.345 17.528 1.00 11.46 HETATM 8154 C6N NDP 1 4.005 1.748 18.602 1.00 12.11 HETATM 8155 P2B NDP 1 7.584 -11.626 25.952 1.00 13.18 HETATM 8156 O1X NDP 1 8.540 -12.200 26.975 1.00 15.49 HETATM 8157 O2X NDP 1 6.162 -12.049 26.180 1.00 13.31 HETATM 8158 O3X NDP 1 8.073 -11.835 24.534 1.00 13.10 ......and following is the part of .rtp file for details of residue NDP [ NDPH ] [ atoms ] AP P 0.76000 0 AO1P OM -0.63500 0 AO2P OM -0.63500 0 AO5* OA -0.36000 0 O3P OA -0.26000 1 NP P 0.76000 1 NO1P OM -0.63500 1 NO2P OM -0.63500 1 NO5* OA -0.36000 1 AC5* CH2 0.00000 2 AC4* CH1 0.16000 3 AO4* OA -0.36000 3 AC1* CH1 0.20000 3 AN9 NR -0.20000 4 AC4 C 0.20000 4 AN3 NR -0.36000 5 AC2 CR1 0.36000 5 AN1 NR -0.36000 6 AC6 C 0.36000 6 AN6 NT -0.83000 7 AH61 H 0.41500 7 AH62 H 0.41500 7 AC5 C 0.00000 8 AN7 NR -0.36000 8 AC8 CR1 0.36000 8 AC2* CH1 0.15000 9 AO2* OA -0.36000 9 AP2* P 0.63000 9 AO6* OM -0.63500 9 AO7* OM -0.63500 9 AO8* OA -0.54800 9 AH8* H 0.39800 9 AC3* CH1 0.15000 10 AO3* OA -0.54800 10 AH3* H 0.39800 10 NC5* CH2 0.00000 11 NC4* CH1 0.16000 12 NO4* OA -0.36000 12 NC1* CH1 0.20000 12 NN1 NR -0.20000 13 NC6 CR1 0.20000 13 NC2 CR1 0.00000 13 NC3 C 0.00000 13 NC4 CH2 0.00000 13 NC5 CR1 0.00000 13 NC7 C 0.38000 14 NO7 O -0.38000 14 NN7 NT -0.83000 15 NH71 H 0.41500 15 NH72 H 0.41500 15 NC2* CH1 0.15000 16 NO2* OA -0.54800 16 NH2* H 0.39800 16 NC3* CH1 0.15000 17 NO3* OA -0.54800 17 NH3* H 0.39800 17 are those file indicating some error like atom name are different in two files, is this the reason for my error or I have to think in some other way. Any advice would be of great help. With Thanx, Vivek 2008/8/13 vivek sharma <[EMAIL PROTECTED]> > Hi Nahren, > Thanx for your help, I opened the pdb file with swisspdb viewer and then > tried the pdb2gmx command over that pdb file and got the following error. > > Total mass 28295.072 a.m.u. > Total charge 1.000 e > Writing topology > Processing chain 5 'E' (372 atoms, 9 residues) > There are 0 donors and 0 acceptors > There are 0 hydrogen bonds > Warning: 'NDP' not found in residue topology database, trying to use 'NDPH' > > ------------------------------------------------------- > Program pdb2gmx, VERSION 3.3.3 > Source code file: pdb2gmx.c, line: 421 > > Fatal error: > Atom PA in residue NDPH 1 not found in rtp entry with 56 atoms > while sorting atoms > ------------------------------------------------------- > > and the error for the all atom forcefield were as follow. > > ------------------------------------------------------- > Program pdb2gmx, VERSION 3.3.3 > Source code file: resall.c, line: 436 > > Fatal error: > Residue 'NDP' not found in residue topology database > > ------------------------------------------------------- > > > any advice for this will be of great help for me. > > Thanx, > Vivek > > 2008/8/12 nahren manuel <[EMAIL PROTECTED]> > > Dear Vivek, >> you just have to download swisspdb and open your pdb file. Thats all you >> got to do and It is more than enough. If you have more than 2/3 residues >> missing then, make sure the Ramachandran plots are fine. Also try a simple >> minimization before begining gromacs. >> >> nahren >> >> --- On *Tue, 8/12/08, vivek sharma <[EMAIL PROTECTED]>* wrote: >> >> From: vivek sharma <[EMAIL PROTECTED]> >> Subject: Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in >> residue PHE270 while adding hydrogens >> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> >> Date: Tuesday, August 12, 2008, 6:34 PM >> >> >> Hi David, >> Thanx a lot again. can you please tell me the criteria or the standards to >> do such correction or can you suggest some link or tutorial for the same? >> whether swiss pdb can help in such cases? >> >> With Thanx, >> Vivek >> >> >> >> 2008/8/12 David van der Spoel <[EMAIL PROTECTED]> >> >>> vivek sharma wrote: >>> >>>> Hi There, >>>> >>>> I am new to molecular dynamics and GROMACS. >>>> While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the >>>> command.... >>>> >>>> pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen >>>> -water spce >>>> >>>> I got the following in the last of error..... >>>> ...... >>>> ...... >>>> ...... >>>> ....... >>>> N-terminus: NH3+ >>>> C-terminus: COO- >>>> WARNING: atom CE2 not found in residue 270 while adding atom >>>> >>>> ------------------------------------------------------- >>>> Program pdb2gmx, VERSION 3.3.3 >>>> Source code file: genhydro.c, line: 304 >>>> >>>> Fatal error: >>>> Atom CE2 not found in residue PHE270 while adding hydrogens >>>> ------------------------------------------------------- >>>> I tried the same with different force field and water models, but >>>> getting the same error again and again. >>>> any suggestion will be highly appreciated. >>>> >>> >>> You have an incorrect pdb file. An atom is missing. You have to fix it >>> yourself. >>> >>>> >>>> >>>> With thanx, >>>> Vivek >>>> >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> 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 [EMAIL PROTECTED] >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>> >>> >>> >>> _______________________________________________ >>> 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 [EMAIL PROTECTED] >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> _______________________________________________ >> gmx-users mailing list [EMAIL >> PROTECTED]://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 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 [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > >
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