Hi Mark<div><br></div><div>Thanks for the rtp definitions. I added the rtp defs to aminoacids.rtp and renamed residue and atom names in pdb file. </div><div><br></div><div>But pdb2gmx is still complaining about the terminal groups. It seems to have picked up ACE, but not CT3. </div>
<div>pdb2gmx error message and modified pdb file are listed below. Any idea ? Do I need to modify .c.tdb ? If so, do you have that entry as well :) ? </div><div><br></div><div>Thanks </div><div>Sandeep </div><div><br></div>
<div>=============pdb2gmx error=======================================</div><div><div>Back Off! I just backed up topol.top to ./#topol.top.3#</div><div>Processing chain 1 (32 atoms, 4 residues)</div><div>There are 3 donors and 3 acceptors</div>
<div>There are 4 hydrogen bonds</div><div>Identified residue ACE1 as a starting terminus.</div><div>Warning: Residue CT32 in chain has different type (Other) from starting residue ACE1 (Protein).</div><div>Identified residue ALA2 as a ending terminus.</div>
<div>8 out of 8 lines of specbond.dat converted successfully</div><div>Start terminus ACE-1: NH3+</div><div>End terminus ALA-2: COO-</div><div><br></div><div>-------------------------------------------------------</div><div>
Program pdb2gmx_d, VERSION 4.5.4</div><div>Source code file: pdb2top.c, line: 1070</div><div><br></div><div>Fatal error:</div><div>atom N not found in buiding block 1ACE while combining tdb and rtp</div><div>For more information and tips for troubleshooting, please check the GROMACS</div>
<div>website at <a href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></div><div>-------------------------------------------------------</div></div><div>================pdb2gmx error====================================</div>
<div><br></div><div>================modified pdb=====================================</div><div><div><div>REMARK NONE * </div><div>REMARK DATE: 8/10/11 5:30:23 CREATED BY USER: ss2029 </div>
<div><b>ATOM 1 CT3 ACE 1 -2.160 0.537 0.930 1.00 0.00 DIAL</b></div><div><b>ATOM 2 HT1 ACE 1 -2.466 0.003 0.005 1.00 0.00 DIAL</b></div><div><b>ATOM 3 HT2 ACE 1 -2.562 1.572 0.910 1.00 0.00 DIAL</b></div>
<div><b>ATOM 4 HT3 ACE 1 -2.562 0.001 1.816 1.00 0.00 DIAL</b></div><div><b>ATOM 5 C ACE 1 -0.672 0.582 1.009 1.00 0.00 DIAL</b></div><div><b>ATOM 6 O ACE 1 -0.105 1.128 1.954 1.00 0.00 DIAL</b></div>
<div>ATOM 7 N ALA 1 0.000 0.000 0.000 1.00 0.00 DIAL</div><div>ATOM 8 HN ALA 1 -0.453 -0.444 -0.769 1.00 0.00 DIAL</div><div>ATOM 9 CA ALA 1 1.459 0.000 0.000 1.00 0.00 DIAL</div>
<div>ATOM 10 HA ALA 1 1.812 -0.497 0.897 1.00 0.00 DIAL</div><div>ATOM 11 CB ALA 1 1.949 -0.834 -1.207 1.00 0.00 DIAL</div><div>ATOM 12 HB1 ALA 1 1.514 -1.854 -1.155 1.00 0.00 DIAL</div>
<div>ATOM 13 HB2 ALA 1 1.628 -0.373 -2.167 1.00 0.00 DIAL</div><div>ATOM 14 HB3 ALA 1 3.056 -0.932 -1.214 1.00 0.00 DIAL</div><div>ATOM 15 C ALA 1 2.096 1.401 0.000 1.00 0.00 DIAL</div>
<div>ATOM 16 O ALA 1 1.425 2.432 0.000 1.00 0.00 DIAL</div><div>ATOM 17 N ALA 2 3.451 1.458 0.000 1.00 0.00 DIAL</div><div>ATOM 18 HN ALA 2 3.954 0.594 0.000 1.00 0.00 DIAL</div>
<div>ATOM 19 CA ALA 2 4.276 2.664 0.000 1.00 0.00 DIAL</div><div>ATOM 20 HA ALA 2 4.065 3.236 -0.897 1.00 0.00 DIAL</div><div>ATOM 21 CB ALA 2 3.864 3.539 1.207 1.00 0.00 DIAL</div>
<div>ATOM 22 HB1 ALA 2 2.776 3.756 1.155 1.00 0.00 DIAL</div><div>ATOM 23 HB2 ALA 2 4.063 3.014 2.167 1.00 0.00 DIAL</div><div>ATOM 24 HB3 ALA 2 4.407 4.508 1.214 1.00 0.00 DIAL</div>
<div>ATOM 25 C ALA 2 5.791 2.399 0.000 1.00 0.00 DIAL</div><div>ATOM 26 O ALA 2 6.597 3.328 0.000 1.00 0.00 DIAL</div><div><b>ATOM 27 N CT3 2 6.175 1.110 0.000 1.00 0.00 DIAL</b></div>
<div><b>ATOM 28 HN CT3 2 5.528 0.351 0.000 1.00 0.00 DIAL</b></div><div><b>ATOM 29 CT CT3 2 7.566 0.777 0.000 1.00 0.00 DIAL</b></div><div><b>ATOM 30 HT1 CT3 2 8.048 1.201 0.907 1.00 0.00 DIAL</b></div>
</div><div><div><b>ATOM 31 HT2 CT3 2 7.683 -0.327 0.000 1.00 0.00 DIAL</b></div><div><b>ATOM 32 HT3 CT3 2 8.048 1.201 -0.907 1.00 0.00 DIAL</b></div><div>TER 33 CT3 2</div>
<div>END</div></div><div>================modified pdb=====================================</div></div><div><br></div><div><br></div><div><br><br><div class="gmail_quote">On Fri, Sep 9, 2011 at 2:52 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div class="im">On 9/09/2011 8:05 AM, Sandeep Somani wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi<br>
<br>
I am trying to set up a simulation for dialanine using charmm27 ff but am getting errors in pdb2gmx due to missing definitions in rtp file.<br>
<br>
I created the pdb file (below) using Charmm for the sequence ACE-ALA-ALA-CT3.<br>
<br>
pdb2gmx recognizes ALA atoms but not those of the terminal groups ACE and CT3.<br>
</blockquote>
<br></div>
Yes, CHARMM in GROMACS has lacked these for some time. I asked over a year ago for them to be added, but that hasn't happened. You can add<br>
<br>
[ ACE ]<br>
[ atoms ]<br>
CT3 CT3 -0.270 0<br>
HT1 HA 0.090 1<br>
HT2 HA 0.090 2<br>
HT3 HA 0.090 3<br>
C C 0.510 4<br>
O O -0.510 5<br>
[ bonds ]<br>
C CT3<br>
C +N<br>
CT3 HT31<br>
CT3 HT32<br>
CT3 HT33<br>
O C<br>
[ impropers ]<br>
C CT3 +N O<br>
<br>
[ CT3 ]<br>
; this can also be done with the .c.tdb, but the atom naming is different<br>
; and this can matter<br>
[ atoms ]<br>
N NH1 -0.470 0<br>
HN H 0.310 1<br>
CT CT3 -0.110 2<br>
HT1 HA 0.090 3<br>
HT2 HA 0.090 4<br>
HT3 HA 0.090 5<br>
[ bonds ]<br>
-C N<br>
N HN<br>
N CAT<br>
CT HT1<br>
CT HT2<br>
CT HT3<br>
<br>
[ impropers ]<br>
N -C CAT HN<br>
-C CAT N -O<br>
<br>
to the end of aminoacids.rtp in a local copy of the charmm27.ff folder to make this work.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Does someone have the appropriate definitions for these residues ?<br>
( I have tried <a href="http://swissparam.ch/" target="_blank">http://swissparam.ch/</a> to generate an itp file for the molecule, but upon using it in GMX it does not give the same energy as that from charmm. )<br>
</blockquote>
<br></div>
That will likely be a separate issue.<br>
<br>
Mark<br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</font></blockquote></div><br></div>