<div dir="ltr">Hi There,<br><br>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 <br><br>HETATM 8111 PA NDP 1 8.809 -4.754 22.676 1.00 12.71
<br>HETATM 8112 O1A NDP 1 10.106 -4.137 23.158 1.00 11.98
<br>HETATM 8113 O2A NDP 1 8.869 -5.751 21.580 1.00 13.09
<br>HETATM 8114 O5B NDP 1 8.010 -5.348 23.937 1.00 12.91
<br>HETATM 8115 C5B NDP 1 6.913 -6.239 23.752 1.00 12.91
<br>HETATM 8116 C4B NDP 1 6.493 -6.754 25.120 1.00 10.44
<br>HETATM 8117 O4B NDP 1 5.292 -7.535 24.969 1.00 13.02
<br>HETATM 8118 C3B NDP 1 7.588 -7.667 25.612 1.00 10.90
<br>HETATM 8119 O3B NDP 1 7.552 -7.543 27.047 1.00 12.99
<br>HETATM 8120 C2B NDP 1 7.086 -9.053 25.407 1.00 12.38
<br>HETATM 8121 O2B NDP 1 7.660 -10.046 26.246 1.00 13.11
<br>HETATM 8122 C1B NDP 1 5.579 -8.877 25.356 1.00 12.53
<br>HETATM 8123 N9A NDP 1 4.817 -9.905 24.673 1.00 11.65
<br>HETATM 8124 C8A NDP 1 5.033 -10.388 23.429 1.00 10.38
<br>HETATM 8125 N7A NDP 1 4.132 -11.360 23.119 1.00 11.50
<br>HETATM 8126 C5A NDP 1 3.332 -11.498 24.179 1.00 10.26
<br>HETATM 8127 C6A NDP 1 2.217 -12.337 24.568 1.00 11.19
<br>HETATM 8128 N6A NDP 1 1.746 -13.251 23.689 1.00 12.10
<br>HETATM 8129 N1A NDP 1 1.678 -12.169 25.805 1.00 11.24
<br>HETATM 8130 C2A NDP 1 2.130 -11.262 26.690 1.00 10.83
<br>HETATM 8131 N3A NDP 1 3.161 -10.439 26.428 1.00 10.06
<br>HETATM 8132 C4A NDP 1 3.776 -10.558 25.154 1.00 11.15
<br>HETATM 8133 O3 NDP 1 7.769 -3.631 22.173 1.00 12.62
<br>HETATM 8134 PN NDP 1 7.989 -2.036 22.130 1.00 12.08
<br>HETATM 8135 O1N NDP 1 8.430 -1.526 23.461 1.00 11.89
<br>HETATM 8136 O2N NDP 1 8.741 -1.692 20.889 1.00 11.73
<br>HETATM 8137 O5D NDP 1 6.467 -1.533 21.886 1.00 12.66
<br>HETATM 8138 C5D NDP 1 5.611 -1.361 23.020 1.00 11.65
<br>HETATM 8139 C4D NDP 1 4.298 -0.748 22.582 1.00 11.67
<br>HETATM 8140 O4D NDP 1 4.556 0.487 21.875 1.00 12.21
<br>HETATM 8141 C3D NDP 1 3.548 -1.649 21.637 1.00 11.97
<br>HETATM 8142 O3D NDP 1 2.175 -1.497 22.010 1.00 11.22
<br>HETATM 8143 C2D NDP 1 3.579 -0.984 20.290 1.00 12.02
<br>HETATM 8144 O2D NDP 1 2.475 -1.229 19.433 1.00 11.31
<br>HETATM 8145 C1D NDP 1 3.974 0.454 20.593 1.00 12.46
<br>HETATM 8146 N1N NDP 1 4.714 1.092 19.529 1.00 11.43
<br>HETATM 8147 C2N NDP 1 6.045 0.998 19.502 1.00 11.26
<br>HETATM 8148 C3N NDP 1 6.724 1.599 18.453 1.00 10.05
<br>HETATM 8149 C7N NDP 1 8.217 1.540 18.362 1.00 11.67
<br>HETATM 8150 O7N NDP 1 8.756 2.105 17.403 1.00 11.17
<br>HETATM 8151 N7N NDP 1 8.916 0.848 19.266 1.00 11.33
<br>HETATM 8152 C4N NDP 1 6.022 2.270 17.471 1.00 10.99
<br>HETATM 8153 C5N NDP 1 4.641 2.345 17.528 1.00 11.46
<br>HETATM 8154 C6N NDP 1 4.005 1.748 18.602 1.00 12.11
<br>HETATM 8155 P2B NDP 1 7.584 -11.626 25.952 1.00 13.18
<br>HETATM 8156 O1X NDP 1 8.540 -12.200 26.975 1.00 15.49
<br>HETATM 8157 O2X NDP 1 6.162 -12.049 26.180 1.00 13.31
<br>HETATM 8158 O3X NDP 1 8.073 -11.835 24.534 1.00 13.10<br><br>......and following is the part of .rtp file for details of residue NDP<br><br>[ NDPH ]<br> [ atoms ]<br> AP P 0.76000 0<br> AO1P OM -0.63500 0<br>
AO2P OM -0.63500 0<br> AO5* OA -0.36000 0<br> O3P OA -0.26000 1<br> NP P 0.76000 1<br> NO1P OM -0.63500 1<br> NO2P OM -0.63500 1<br> NO5* OA -0.36000 1<br>
AC5* CH2 0.00000 2<br> AC4* CH1 0.16000 3<br> AO4* OA -0.36000 3<br> AC1* CH1 0.20000 3<br> AN9 NR -0.20000 4<br> AC4 C 0.20000 4<br> AN3 NR -0.36000 5<br>
AC2 CR1 0.36000 5<br> AN1 NR -0.36000 6<br> AC6 C 0.36000 6<br> AN6 NT -0.83000 7<br> AH61 H 0.41500 7<br> AH62 H 0.41500 7<br> AC5 C 0.00000 8<br>
AN7 NR -0.36000 8<br> AC8 CR1 0.36000 8<br> AC2* CH1 0.15000 9<br> AO2* OA -0.36000 9<br> AP2* P 0.63000 9<br> AO6* OM -0.63500 9<br> AO7* OM -0.63500 9<br>
AO8* OA -0.54800 9<br> AH8* H 0.39800 9<br> AC3* CH1 0.15000 10<br> AO3* OA -0.54800 10<br> AH3* H 0.39800 10<br> NC5* CH2 0.00000 11<br> NC4* CH1 0.16000 12<br>
NO4* OA -0.36000 12<br> NC1* CH1 0.20000 12<br> NN1 NR -0.20000 13<br> NC6 CR1 0.20000 13<br> NC2 CR1 0.00000 13<br> NC3 C 0.00000 13<br> NC4 CH2 0.00000 13<br>
NC5 CR1 0.00000 13<br> NC7 C 0.38000 14<br> NO7 O -0.38000 14<br> NN7 NT -0.83000 15<br> NH71 H 0.41500 15<br> NH72 H 0.41500 15<br> NC2* CH1 0.15000 16<br>
NO2* OA -0.54800 16<br> NH2* H 0.39800 16<br> NC3* CH1 0.15000 17<br> NO3* OA -0.54800 17<br> NH3* H 0.39800 17<br><br>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. <br>
Any advice would be of great help.<br><br>With Thanx,<br>Vivek<br><br><div class="gmail_quote">2008/8/13 vivek sharma <span dir="ltr"><<a href="mailto:viveksharma.iitb@gmail.com">viveksharma.iitb@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div dir="ltr">Hi Nahren,<br>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.<br>
<br>Total mass 28295.072 a.m.u.<br>Total charge 1.000 e<br>
Writing topology<br>Processing chain 5 'E' (372 atoms, 9 residues)<br>There are 0 donors and 0 acceptors<br>There are 0 hydrogen bonds<br>Warning: 'NDP' not found in residue topology database, trying to use 'NDPH'<div class="Ih2E3d">
<br>
<br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 3.3.3<br></div>Source code file: pdb2gmx.c, line: 421<br><br>Fatal error:<br>Atom PA in residue NDPH 1 not found in rtp entry with 56 atoms<br>
while sorting atoms<br>-------------------------------------------------------<br><br>and the error for the all atom forcefield were as follow.<div class="Ih2E3d"><br><br>-------------------------------------------------------<br>
Program pdb2gmx, VERSION 3.3.3<br></div>Source code file: resall.c, line: 436<br><br>Fatal error:<br>Residue 'NDP' not found in residue topology database<br><br>-------------------------------------------------------<br>
<br><br>any advice for this will be of great help for me.<br><br>Thanx,<br>Vivek<br><br><div class="gmail_quote">2008/8/12 nahren manuel <span dir="ltr"><<a href="mailto:meetnahren@yahoo.com" target="_blank">meetnahren@yahoo.com</a>></span><div>
<div></div><div class="Wj3C7c"><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top">
<div>Dear Vivek,</div>
<div>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.</div>
<div> </div>
<div>nahren<br><br>--- On <b>Tue, 8/12/08, vivek sharma <i><<a href="mailto:viveksharma.iitb@gmail.com" target="_blank">viveksharma.iitb@gmail.com</a>></i></b> wrote:<br></div>
<blockquote style="border-left: 2px solid rgb(16, 16, 255); padding-left: 5px; margin-left: 5px;">From: vivek sharma <<a href="mailto:viveksharma.iitb@gmail.com" target="_blank">viveksharma.iitb@gmail.com</a>><br>Subject: Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens<br>
To: "Discussion list for GROMACS users" <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>Date: Tuesday, August 12, 2008, 6:34 PM<div><div></div><div><br>
<br>
<div>
<div dir="ltr">Hi David,<br>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?<br>whether swiss pdb can help in such cases?<br>
<br>With Thanx,<br>Vivek<br><br><br><br>
<div class="gmail_quote">2008/8/12 David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se" rel="nofollow" target="_blank">spoel@xray.bmc.uu.se</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>
<div></div>
<div>vivek sharma wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi There,<br><br>I am new to molecular dynamics and GROMACS.<br>While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command....<br>
<br> pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce<br><br>I got the following in the last of error.....<br>......<br>......<br>......<br>.......<br>N-terminus: NH3+<br>C-terminus: COO-<br>
WARNING: atom CE2 not found in residue 270 while adding atom<br><br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 3.3.3<br>Source code file: genhydro.c, line: 304<br><br>Fatal error:<br>
Atom CE2 not found in residue PHE270 while adding hydrogens<br>-------------------------------------------------------<br> I tried the same with different force field and water models, but getting the same error again and
again.<br>any suggestion will be highly appreciated.<br></blockquote><br></div></div>You have an incorrect pdb file. An atom is missing. You have to fix it yourself.<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br><br>With thanx,<br>Vivek<br><br>------------------------------------------------------------------------<br>
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