Hi Justin and Mark,<div><br></div><div>Thank you so much for your replies. Mark, would you mind clarifying what you mean? What exactly should I be looking for in the ffbonded.itp file? I'm not sure why those bonded parameters in particular were overridden... I didn't intend to modify anything!</div>
<div><br></div><div>Perhaps it would help if I gave a more complete description of my system. I'm using the oplsaa force field to model a simple alkanethiol chain. I've defined a new residue as follows:</div><div>
<br></div><div><div>[ ALK ]</div><div> [ atoms ]</div><div> CA opls_139 -0.180 1</div><div> HAA opls_140 0.060 1</div><div> HAB opls_140 0.060 1</div><div> HAC opls_140 0.060 1</div>
<div> CB opls_139 -0.120 2</div><div> HBA opls_140 0.060 2</div><div> HBB opls_140 0.060 2</div><div> CC opls_139 -0.120 3</div><div> HCA opls_140 0.060 3</div><div>
HCB opls_140 0.060 3</div><div> CD opls_139 -0.120 4</div><div> HDA opls_140 0.060 4</div><div> HDB opls_140 0.060 4</div><div> CE opls_139 -0.120 5</div><div> HEA opls_140 0.060 5</div>
<div> HEB opls_140 0.060 5</div><div> CF opls_139 -0.120 6</div><div> HFA opls_140 0.060 6</div><div> HFB opls_140 0.060 6</div><div> CG opls_139 -0.120 7</div><div>
HGA opls_140 0.060 7</div><div> HGB opls_140 0.060 7</div><div> CH opls_139 -0.120 8</div><div> HHA opls_140 0.060 8</div><div> HHB opls_140 0.060 8</div><div> CI opls_139 -0.120 9</div>
<div> HIA opls_140 0.060 9</div><div> HIB opls_140 0.060 9</div><div> CJ opls_139 -0.120 10</div><div> HJA opls_140 0.060 10</div><div> HJB opls_140 0.060 10</div>
<div> CK opls_139 -0.120 11</div><div> HKA opls_140 0.060 11</div><div> HKB opls_140 0.060 11</div><div> CL opls_206 -0.120 12</div><div> HLA opls_140 0.060 12</div>
<div> HLB opls_140 0.060 12</div><div> SA opls_200 -0.335 13</div><div> HS opls_204 0.155 13</div><div> [ bonds ]</div><div> CA HAA</div><div><div> CA HAB</div><div> CA HAC</div>
<div> CA CB</div><div> CB HBA</div><div> CB HBB</div><div> CB CC</div><div> CC HCA</div><div> CC HCB</div><div> CC CD</div><div> CD HDA</div><div> CD HDB</div><div> CD CE</div>
<div> CE HEA</div><div> CE HEB</div><div> CE CF</div><div> CF HFA</div><div> CF HFB</div><div> CF CG</div><div> CG HGA</div><div> CG HGB</div><div> CG CH</div><div> CH HHA</div>
<div> CH HHB</div><div> CH CI</div><div> CI HIA</div><div> CI HIB</div><div> CI CJ</div><div> CJ HJA</div><div> CJ HJB</div><div> CJ CK</div><div> CK HKA</div><div> CK HKB</div>
<div> CK CL</div><div> CL HLA</div><div> CL HLB</div><div> CL SA</div><div> SA HS</div></div><div><br></div><div><br></div><div>In ffbonded.itp, I've defined the following bondtypes:</div>
<div><br></div><div><br></div><div><div>; begin Olivia-defined bondtypes</div><div> CA HAA 1 0.10800 284512.0 ; spring constant came from OPLS C* HC bondtype</div><div> CA HAB 1 0.10800 284512.0</div>
<div> CA HAC 1 0.10800 284512.0</div><div> CA CB 1 0.15300 265265.6 ; spring constant came from OPLS C C3 bondtype</div><div> CB HBA 1 0.10800 284512.0</div><div> CB HBB 1 0.10800 284512.0</div>
<div> CB CC 1 0.15300 265265.6</div><div> CC HCA 1 0.10800 284512.0</div><div> CC HCB 1 0.10800 284512.0</div><div> CC CD 1 0.15300 265265.6</div><div> CD HDA 1 0.10800 284512.0</div>
<div> CD HDB 1 0.10800 284512.0</div><div> CD CE 1 0.15300 265265.6</div><div> CE HEA 1 0.10800 284512.0</div><div> CE HEB 1 0.10800 284512.0</div><div> CE CF 1 0.15300 265265.6</div>
<div> CF HFA 1 0.10800 284512.0</div><div> CF HFB 1 0.10800 284512.0</div><div> CF CG 1 0.15300 265265.6</div><div> CG HGA 1 0.10800 284512.0</div><div> CG HGB 1 0.10800 284512.0</div>
<div> CG CH 1 0.15300 265265.6</div><div> CH HHA 1 0.10800 284512.0</div><div> CH HHB 1 0.10800 284512.0</div><div> CH CI 1 0.15300 265265.6</div><div> CI HIA 1 0.10800 284512.0</div>
<div> CI HIB 1 0.10800 284512.0</div><div> CI CJ 1 0.15300 265265.6</div><div> CJ HJA 1 0.10800 284512.0</div><div> CJ HJB 1 0.10800 284512.0</div><div> CJ CK 1 0.15300 265265.6</div>
<div> CK HKA 1 0.10800 284512.0</div><div> CK HKB 1 0.10800 284512.0</div><div> CK CL 1 0.15300 265265.6</div><div> CL HLA 1 0.10800 284512.0</div><div> CL HLB 1 0.10800 284512.0</div>
<div> CL SA 1 0.18200 284512.0 ; not sure what the spring constant should be here... will peruse literature!</div></div><div><br></div><div><br></div><div>Here is my topology file (different from the last one I posted, since that was for a customized forcefield I had designed from scratch... I have since abandoned that pursuit, and here I am using the predefined opls parameters.)</div>
<div><br></div><div><div>; Include forcefield parameters</div><div>#include "oplsaa.ff/forcefield.itp"</div><div><br></div><div>[ moleculetype ]</div><div>; Name nrexcl</div><div>Protein 3</div>
<div><br></div><div>[ atoms ]</div><div>; nr type resnr residue atom cgnr charge mass typeB chargeB massB</div><div>; residue 1 ALK rtp ALK q -0.2</div><div> 1 opls_139 1 ALK CA 1 -0.18 12.011 ; qtot -0.18</div>
<div> 2 opls_140 1 ALK HAA 1 0.06 1.008 ; qtot -0.12</div><div> 3 opls_140 1 ALK HAB 1 0.06 1.008 ; qtot -0.06</div><div> 4 opls_140 1 ALK HAC 1 0.06 1.008 ; qtot 0</div>
<div> 5 opls_139 1 ALK CB 2 -0.12 12.011 ; qtot -0.12</div><div> 6 opls_140 1 ALK HBA 2 0.06 1.008 ; qtot -0.06</div><div> 7 opls_140 1 ALK HBB 2 0.06 1.008 ; qtot 0</div>
<div> 8 opls_139 1 ALK CC 3 -0.12 12.011 ; qtot -0.12</div><div> 9 opls_140 1 ALK HCA 3 0.06 1.008 ; qtot -0.06</div><div> 10 opls_140 1 ALK HCB 3 0.06 1.008 ; qtot 0</div>
<div> 11 opls_139 1 ALK CD 4 -0.12 12.011 ; qtot -0.12</div><div> 12 opls_140 1 ALK HDA 4 0.06 1.008 ; qtot -0.06</div><div> 13 opls_140 1 ALK HDB 4 0.06 1.008 ; qtot 0</div>
<div> 14 opls_139 1 ALK CE 5 -0.12 12.011 ; qtot -0.12</div><div> 15 opls_140 1 ALK HEA 5 0.06 1.008 ; qtot -0.06</div><div> 16 opls_140 1 ALK HEB 5 0.06 1.008 ; qtot 0</div>
<div> 17 opls_139 1 ALK CF 6 -0.12 12.011 ; qtot -0.12</div><div> 18 opls_140 1 ALK HFA 6 0.06 1.008 ; qtot -0.06</div><div> 19 opls_140 1 ALK HFB 6 0.06 1.008 ; qtot 0</div>
<div> 20 opls_139 1 ALK CG 7 -0.12 12.011 ; qtot -0.12</div><div> 21 opls_140 1 ALK HGA 7 0.06 1.008 ; qtot -0.06</div><div> 22 opls_140 1 ALK HGB 7 0.06 1.008 ; qtot 0</div>
<div> 23 opls_139 1 ALK CH 8 -0.12 12.011 ; qtot -0.12</div><div> 24 opls_140 1 ALK HHA 8 0.06 1.008 ; qtot -0.06</div><div> 25 opls_140 1 ALK HHB 8 0.06 1.008 ; qtot 0</div>
<div> 26 opls_139 1 ALK CI 9 -0.12 12.011 ; qtot -0.12</div><div> 27 opls_140 1 ALK HIA 9 0.06 1.008 ; qtot -0.06</div><div> 28 opls_140 1 ALK HIB 9 0.06 1.008 ; qtot 0</div>
<div> 29 opls_139 1 ALK CJ 10 -0.12 12.011 ; qtot -0.12</div><div> 30 opls_140 1 ALK HJA 10 0.06 1.008 ; qtot -0.06</div><div> 31 opls_140 1 ALK HJB 10 0.06 1.008 ; qtot 0</div>
<div> 32 opls_139 1 ALK CK 11 -0.12 12.011 ; qtot -0.12</div><div> 33 opls_140 1 ALK HKA 11 0.06 1.008 ; qtot -0.06</div><div> 34 opls_140 1 ALK HKB 11 0.06 1.008 ; qtot 0</div>
<div> 35 opls_206 1 ALK CL 12 -0.12 12.011 ; qtot -0.12</div><div> 36 opls_140 1 ALK HLA 12 0.06 1.008 ; qtot -0.06</div><div> 37 opls_140 1 ALK HLB 12 0.06 1.008 ; qtot 0</div>
<div> 38 opls_200 1 ALK SA 13 -0.335 32.06 ; qtot -0.335</div><div> 39 opls_204 1 ALK HS 13 0.155 1.008 ; qtot -0.18</div><div><br></div><div>[ bonds ]</div>
<div>; ai aj funct c0 c1 c2 c3</div><div> 1 2 1</div><div> 1 3 1</div><div> 1 4 1</div><div> 1 5 1</div><div> 5 6 1</div>
<div> 5 7 1</div><div> 5 8 1</div></div><div><br></div><div>....... etc. .......</div><div><br></div><div><div>; Include Position restraint file</div><div>#ifdef POSRES</div><div>#include "posre.itp"</div>
<div>#endif</div><div><br></div><div>; Include water topology</div><div>#include "oplsaa.ff/tip3p.itp"</div><div><br></div><div>#ifdef POSRES_WATER</div><div>; Position restraint for each water oxygen</div><div>
[ position_restraints ]</div><div>; i funct fcx fcy fcz</div><div> 1 1 1000 1000 1000</div><div>#endif</div><div><br></div><div>; Include topology for ions</div><div>#include "oplsaa.ff/ions.itp"</div>
<div><br></div><div>[ system ]</div><div>; Name</div><div>Protein</div><div><br></div><div>[ molecules ]</div><div>; Compound #mols</div><div>Protein 1</div></div><div><br></div><div><br></div><div>I'm so sorry to inundate you with information, but I hope this might help us get to the root of the problem!! I've been staring at this for days. :)</div>
<div><br></div><div>Thanks again,</div><div>Olivia</div><div><br></div><br><div class="gmail_quote">On Tue, Nov 1, 2011 at 8:48 PM, 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 text="#000000" bgcolor="#FFFFFF"><div class="im">
On 2/11/2011 8:32 AM, Olivia Waring wrote:
<blockquote type="cite"><span style="color:rgb(51, 51, 51);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255, 255, 255)">
<div><span style="color:rgb(51, 51, 51);font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)">Dear Gromacs users,</span></div>
<span style="color:rgb(51, 51, 51);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255, 255, 255)">
<div><span style="color:rgb(51, 51, 51);font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)"><br>
</span></div>
First of all, many thanks to Justin for his assistance with my
previous question.
<div><br>
</div>
<div>I have defined a new residue type in the oplsaa force
field, changing the aminoacids.rtp file accordingly. pdb2gmx
worked just fine; but when I try to preprocess, I get the
following output: </div>
<div><br>
</div>
<div>
<div>WARNING 1 [file ffbonded.itp, line 58]:</div>
</div>
</span></span></blockquote>
<br></div>
You'll need to inspect at and before this line in this file to
diagnose.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div><div class="h5"><br>
<br>
<blockquote type="cite"><span style="color:rgb(51, 51, 51);font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)"><span style="color:rgb(51, 51, 51);font-family:arial, sans-serif;font-size:13px;background-color:rgb(255, 255, 255)">
<div>
<div> Overriding Bond parameters.</div>
<div><br>
</div>
<div> old: 0.1229 476976 0.1229 476976</div>
<div> new: C O 1 0.13270 179075.2</div>
<div><br>
</div>
<div><br>
</div>
<div>WARNING 2 [file ffbonded.itp, line 64]:</div>
<div> Overriding Bond parameters.</div>
<div><br>
</div>
<div> old: 0.1522 265266 0.1522 265266</div>
<div> new: C CT 1 0.14950 265265.6</div>
<div><br>
</div>
<div><br>
</div>
<div>WARNING 3 [file ffbonded.itp, line 67]:</div>
<div> Overriding Bond parameters.</div>
<div><br>
</div>
<div> old: 0.149 334720 0.149 334720</div>
<div> new: CA C 1 0.14240 392459.2</div>
<div><br>
</div>
<div><br>
</div>
<div>WARNING 4 [file ffbonded.itp, line 73]:</div>
<div> Overriding Bond parameters.</div>
<div><br>
</div>
<div> old: 0.1419 374050 0.1419 374050</div>
<div> new: C CB 1 0.14240 392459.2</div>
<div><br>
</div>
<div><br>
</div>
<div>-------------------------------------------------------</div>
<div>Program grompp, VERSION 4.5.4</div>
<div>Source code file: topdirs.c, line: 76</div>
<div><br>
</div>
<div>Fatal error:</div>
<div>Invalid bond type 0</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" style="color:rgb(61, 84, 89)" target="_blank">http://www.gromacs.org/Documentation/Errors</a></div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>The error is rather cryptic, and I'm having trouble
tracking it down... I even went to the source code
(topdirs.c), but I'm still not sure where exactly this
"invalid bond type" is being defined. </div>
<div><br>
</div>
<div>Thank you so much for your help,</div>
<div>Olivia</div>
</span></span><br clear="all">
<div><br>
</div>
-- <br>
<div>Olivia Waring (王维娅)</div>
<div>Princeton University '12</div>
<div>AB Chemistry</div>
<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div></div>
<br>--<br>
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Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div>Olivia Waring (王维娅)</div>
<div>Princeton University '12</div>
<div>AB Chemistry</div><br>
</div>