Yes, it's the same error. <div><br></div><div>About the bond types: should they be defined as opls_* in ffbonded.itp, aminoacids.rtp, both, or somewhere else entirely?</div><div><br></div><div>Sorry to be such a nuisance!</div>
<div><br></div><div>Olivia<br><br><div class="gmail_quote">On Wed, Nov 2, 2011 at 4:27 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="HOEnZb"><div class="h5"><br>
<br>
Olivia Waring wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Justin and Mark,<br>
<br>
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!<br>
<br>
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:<br>
<br>
[ ALK ]<br>
[ atoms ]<br>
CA opls_139 -0.180 1<br>
HAA opls_140 0.060 1<br>
HAB opls_140 0.060 1<br>
HAC opls_140 0.060 1<br>
CB opls_139 -0.120 2<br>
HBA opls_140 0.060 2<br>
HBB opls_140 0.060 2<br>
CC opls_139 -0.120 3<br>
HCA opls_140 0.060 3<br>
HCB opls_140 0.060 3<br>
CD opls_139 -0.120 4<br>
HDA opls_140 0.060 4<br>
HDB opls_140 0.060 4<br>
CE opls_139 -0.120 5<br>
HEA opls_140 0.060 5<br>
HEB opls_140 0.060 5<br>
CF opls_139 -0.120 6<br>
HFA opls_140 0.060 6<br>
HFB opls_140 0.060 6<br>
CG opls_139 -0.120 7<br>
HGA opls_140 0.060 7<br>
HGB opls_140 0.060 7<br>
CH opls_139 -0.120 8<br>
HHA opls_140 0.060 8<br>
HHB opls_140 0.060 8<br>
CI opls_139 -0.120 9<br>
HIA opls_140 0.060 9<br>
HIB opls_140 0.060 9<br>
CJ opls_139 -0.120 10<br>
HJA opls_140 0.060 10<br>
HJB opls_140 0.060 10<br>
CK opls_139 -0.120 11<br>
HKA opls_140 0.060 11<br>
HKB opls_140 0.060 11<br>
CL opls_206 -0.120 12<br>
HLA opls_140 0.060 12<br>
HLB opls_140 0.060 12<br>
SA opls_200 -0.335 13<br>
HS opls_204 0.155 13<br>
[ bonds ]<br>
CA HAA<br>
CA HAB<br>
CA HAC<br>
CA CB<br>
CB HBA<br>
CB HBB<br>
CB CC<br>
CC HCA<br>
CC HCB<br>
CC CD<br>
CD HDA<br>
CD HDB<br>
CD CE<br>
CE HEA<br>
CE HEB<br>
CE CF<br>
CF HFA<br>
CF HFB<br>
CF CG<br>
CG HGA<br>
CG HGB<br>
CG CH<br>
CH HHA<br>
CH HHB<br>
CH CI<br>
CI HIA<br>
CI HIB<br>
CI CJ<br>
CJ HJA<br>
CJ HJB<br>
CJ CK<br>
CK HKA<br>
CK HKB<br>
CK CL<br>
CL HLA<br>
CL HLB<br>
CL SA<br>
SA HS<br>
<br>
<br>
In ffbonded.itp, I've defined the following bondtypes:<br>
<br>
<br>
; begin Olivia-defined bondtypes<br>
CA HAA 1 0.10800 284512.0 ; spring constant came from OPLS C* HC bondtype<br>
CA HAB 1 0.10800 284512.0<br>
CA HAC 1 0.10800 284512.0<br>
CA CB 1 0.15300 265265.6 ; spring constant came from OPLS C C3 bondtype<br>
CB HBA 1 0.10800 284512.0<br>
CB HBB 1 0.10800 284512.0<br>
CB CC 1 0.15300 265265.6<br>
CC HCA 1 0.10800 284512.0<br>
CC HCB 1 0.10800 284512.0<br>
CC CD 1 0.15300 265265.6<br>
CD HDA 1 0.10800 284512.0<br>
CD HDB 1 0.10800 284512.0<br>
CD CE 1 0.15300 265265.6<br>
CE HEA 1 0.10800 284512.0<br>
CE HEB 1 0.10800 284512.0<br>
CE CF 1 0.15300 265265.6<br>
CF HFA 1 0.10800 284512.0<br>
CF HFB 1 0.10800 284512.0<br>
CF CG 1 0.15300 265265.6<br>
CG HGA 1 0.10800 284512.0<br>
CG HGB 1 0.10800 284512.0<br>
CG CH 1 0.15300 265265.6<br>
CH HHA 1 0.10800 284512.0<br>
CH HHB 1 0.10800 284512.0<br>
CH CI 1 0.15300 265265.6<br>
CI HIA 1 0.10800 284512.0<br>
CI HIB 1 0.10800 284512.0<br>
CI CJ 1 0.15300 265265.6<br>
CJ HJA 1 0.10800 284512.0<br>
CJ HJB 1 0.10800 284512.0<br>
CJ CK 1 0.15300 265265.6<br>
CK HKA 1 0.10800 284512.0<br>
CK HKB 1 0.10800 284512.0<br>
CK CL 1 0.15300 265265.6<br>
CL HLA 1 0.10800 284512.0<br>
CL HLB 1 0.10800 284512.0<br>
CL SA 1 0.18200 284512.0 ; not sure what the spring constant should be here... will peruse literature!<br>
<br>
<br>
</blockquote>
<br></div></div>
Bond types are not defined by atom name, but rather atom type. If you're using OPLS, then all the types should be opls_* to be valid. I suspect this is at least one source of problem.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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.)<br>
<br>
</blockquote>
<br></div>
Does this topology produce the exact same errors as in your last post?<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
; Include forcefield parameters<br>
#include "oplsaa.ff/forcefield.itp"<br>
<br>
[ moleculetype ]<br>
; Name nrexcl<br>
Protein 3<br>
<br>
[ atoms ]<br>
; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br>
; residue 1 ALK rtp ALK q -0.2<br>
1 opls_139 1 ALK CA 1 -0.18 12.011 ; qtot -0.18<br>
2 opls_140 1 ALK HAA 1 0.06 1.008 ; qtot -0.12<br>
3 opls_140 1 ALK HAB 1 0.06 1.008 ; qtot -0.06<br>
4 opls_140 1 ALK HAC 1 0.06 1.008 ; qtot 0<br>
5 opls_139 1 ALK CB 2 -0.12 12.011 ; qtot -0.12<br>
6 opls_140 1 ALK HBA 2 0.06 1.008 ; qtot -0.06<br>
7 opls_140 1 ALK HBB 2 0.06 1.008 ; qtot 0<br>
8 opls_139 1 ALK CC 3 -0.12 12.011 ; qtot -0.12<br>
9 opls_140 1 ALK HCA 3 0.06 1.008 ; qtot -0.06<br>
10 opls_140 1 ALK HCB 3 0.06 1.008 ; qtot 0<br>
11 opls_139 1 ALK CD 4 -0.12 12.011 ; qtot -0.12<br>
12 opls_140 1 ALK HDA 4 0.06 1.008 ; qtot -0.06<br>
13 opls_140 1 ALK HDB 4 0.06 1.008 ; qtot 0<br>
14 opls_139 1 ALK CE 5 -0.12 12.011 ; qtot -0.12<br>
15 opls_140 1 ALK HEA 5 0.06 1.008 ; qtot -0.06<br>
16 opls_140 1 ALK HEB 5 0.06 1.008 ; qtot 0<br>
17 opls_139 1 ALK CF 6 -0.12 12.011 ; qtot -0.12<br>
18 opls_140 1 ALK HFA 6 0.06 1.008 ; qtot -0.06<br>
19 opls_140 1 ALK HFB 6 0.06 1.008 ; qtot 0<br>
20 opls_139 1 ALK CG 7 -0.12 12.011 ; qtot -0.12<br>
21 opls_140 1 ALK HGA 7 0.06 1.008 ; qtot -0.06<br>
22 opls_140 1 ALK HGB 7 0.06 1.008 ; qtot 0<br>
23 opls_139 1 ALK CH 8 -0.12 12.011 ; qtot -0.12<br>
24 opls_140 1 ALK HHA 8 0.06 1.008 ; qtot -0.06<br>
25 opls_140 1 ALK HHB 8 0.06 1.008 ; qtot 0<br>
26 opls_139 1 ALK CI 9 -0.12 12.011 ; qtot -0.12<br>
27 opls_140 1 ALK HIA 9 0.06 1.008 ; qtot -0.06<br>
28 opls_140 1 ALK HIB 9 0.06 1.008 ; qtot 0<br>
29 opls_139 1 ALK CJ 10 -0.12 12.011 ; qtot -0.12<br>
30 opls_140 1 ALK HJA 10 0.06 1.008 ; qtot -0.06<br>
31 opls_140 1 ALK HJB 10 0.06 1.008 ; qtot 0<br>
32 opls_139 1 ALK CK 11 -0.12 12.011 ; qtot -0.12<br>
33 opls_140 1 ALK HKA 11 0.06 1.008 ; qtot -0.06<br>
34 opls_140 1 ALK HKB 11 0.06 1.008 ; qtot 0<br>
35 opls_206 1 ALK CL 12 -0.12 12.011 ; qtot -0.12<br>
36 opls_140 1 ALK HLA 12 0.06 1.008 ; qtot -0.06<br>
37 opls_140 1 ALK HLB 12 0.06 1.008 ; qtot 0<br>
38 opls_200 1 ALK SA 13 -0.335 32.06 ; qtot -0.335<br>
39 opls_204 1 ALK HS 13 0.155 1.008 ; qtot -0.18<br>
<br>
[ bonds ]<br>
; ai aj funct c0 c1 c2 c3<br>
1 2 1<br>
1 3 1<br>
1 4 1<br>
1 5 1<br>
5 6 1<br>
5 7 1<br>
5 8 1<br>
<br>
....... etc. .......<br>
<br>
; Include Position restraint file<br>
#ifdef POSRES<br>
#include "posre.itp"<br>
#endif<br>
<br>
; Include water topology<br>
#include "oplsaa.ff/tip3p.itp"<br>
<br>
#ifdef POSRES_WATER<br>
; Position restraint for each water oxygen<br>
[ position_restraints ]<br>
; i funct fcx fcy fcz<br>
1 1 1000 1000 1000<br>
#endif<br>
<br>
; Include topology for ions<br>
#include "oplsaa.ff/ions.itp"<br>
<br>
[ system ]<br>
; Name<br>
Protein<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
Protein 1<br>
<br>
<br>
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. :)<br>
<br>
Thanks again,<br>
Olivia<br>
<br>
<br></div></div><div><div class="h5">
On Tue, Nov 1, 2011 at 8:48 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.<u></u>au</a>>> wrote:<br>
<br>
On 2/11/2011 8:32 AM, Olivia Waring wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Gromacs users,<br>
<br>
First of all, many thanks to Justin for his assistance with my<br>
previous question.<br>
<br>
I have defined a new residue type in the oplsaa force field,<br>
changing the aminoacids.rtp file accordingly. pdb2gmx worked just<br>
fine; but when I try to preprocess, I get the following output: <br>
WARNING 1 [file ffbonded.itp, line 58]:<br>
</blockquote>
<br>
You'll need to inspect at and before this line in this file to diagnose.<br>
<br>
Mark<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Overriding Bond parameters.<br>
<br>
old: 0.1229 476976 0.1229 476976<br>
new: C O 1 0.13270 179075.2<br>
<br>
<br>
WARNING 2 [file ffbonded.itp, line 64]:<br>
Overriding Bond parameters.<br>
<br>
old: 0.1522 265266 0.1522 265266<br>
new: C CT 1 0.14950 265265.6<br>
<br>
<br>
WARNING 3 [file ffbonded.itp, line 67]:<br>
Overriding Bond parameters.<br>
<br>
old: 0.149 334720 0.149 334720<br>
new: CA C 1 0.14240 392459.2<br>
<br>
<br>
WARNING 4 [file ffbonded.itp, line 73]:<br>
Overriding Bond parameters.<br>
<br>
old: 0.1419 374050 0.1419 374050<br>
new: C CB 1 0.14240 392459.2<br>
<br>
<br>
------------------------------<u></u>-------------------------<br>
Program grompp, VERSION 4.5.4<br>
Source code file: topdirs.c, line: 76<br>
<br>
Fatal error:<br>
Invalid bond type 0<br>
For more information and tips for troubleshooting, please check<br>
the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/<u></u>Documentation/Errors</a><br>
<br>
<br>
The error is rather cryptic, and I'm having trouble tracking it<br>
down... I even went to the source code (topdirs.c), but I'm still<br>
not sure where exactly this "invalid bond type" is being defined. <br>
Thank you so much for your help,<br>
Olivia<br>
<br>
<br>
-- Olivia Waring (王维娅)<br>
Princeton University '12<br>
AB Chemistry<br>
<br>
<br>
<br>
</blockquote>
<br>
<br>
--<br>
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<br>
<br>
<br>
<br>
-- <br>
Olivia Waring (王维娅)<br>
Princeton University '12<br>
AB Chemistry<br>
<br>
</div></blockquote><div class="im HOEnZb">
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br></div><div class="HOEnZb"><div class="h5">
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