Hi Justin,<br> Presently i too facing the same exact problem. I built the topology for a chromophore in the protein and entered all the new parameters in the .rtp, atp, hdb and defined the bonded and nonbonded parameters. Finally i got the following error.<br>
<br>Fatal error:<br>Atom OXT in residue CRIH 64 was not found in rtp entry CRIH with 27 atoms<br>while sorting atoms.<br><br>By this time if you identified the problem. Please help me too. Thank you.<br>Rama<br><br><div class="gmail_quote">
On Mon, Sep 20, 2010 at 3:00 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: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
Mark Abraham wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<br>
----- Original Message -----<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
Date: Tuesday, September 21, 2010 6:30<br>
Subject: [gmx-users] Problem with pdb2gmx and a new residue<br>
To: Gromacs Users' List <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<br>
><br>
> Hi All,<br>
><br>
> I'm trying to build a topology for a chromophore-containing<br>
> protein using Gromacs 4.5 and OPLS-AA. The chromophore is<br>
> incorporated into the protein's backbone and the parameters all<br>
> come from a reputable publication, so I've done the following:<br>
><br>
> 1. Created a new .rtp entry<br>
> 2. Created an .hdb entry<br>
> 3. Defined all nonbonded parameters for new atomtypes in the<br>
> .atp and ffnonbonded.itp file<br>
> 4. Defined all new bonded parameters in ffbonded.itp<br>
<br>
I think you need to define CRO as Protein in residuetypes.dat so that the pdb2gmx mechanism can deduce that it should form a C-terminal peptide link in the absence of an end-of-chain marker.<br>
<br>
</blockquote>
<br>
I had done that, I forgot to mention it. I tried using my modified residuetypes.dat from both the working directory and in $GMXLIB.<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Similarly, I have a modified peptide in what's become my "system for generating pdb2gmx bugzilla reports", and with 4.5.1 and git head, if I omit the residuetypes.dat definition I see<br>
<br>
Identified residue ALA1 as a starting terminus.<br>
Warning: Residue KCX193 in chain has different type (Other) from starting residue ALA1 (Protein).<br>
Warning: Residue ASP194 in chain has different type (Protein) from starting residue ALA1 (Protein).<br>
Warning: Residue ASP195 in chain has different type (Protein) from starting residue ALA1 (Protein).<br>
Warning: Residue GLU196 in chain has different type (Protein) from starting residue ALA1 (Protein).<br>
Warning: Residue ASN197 in chain has different type (Protein) from starting residue ALA1 (Protein).<br>
More than 5 unidentified residues at end of chain - disabling further warnings.<br>
Identified residue THR192 as a ending terminus.<br>
<snip><br>
-------------------------------------------------------<br>
Program pdb2gmx_master, VERSION 4.5.1-20100916-6d51340<br>
Source code file: ../../../src/kernel/pdb2gmx.c, line: 655<br>
<br>
Fatal error:<br>
Atom OXT in residue VAL 467 was not found in rtp entry VAL with 16 atoms<br>
while sorting atoms.<br>
.<br>
For more information and tips for troubleshooting, please check the GROMACS<br>
website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
<br>
This is a bit different, inasmuch as I see the error on the final residue of the first chain, rather then on the modified residue, as you do. However pdb2gmx should cope better with this case - clearly it's confused in the above messages about non-matching types.<br>
<br>
We should probably file a bugzilla, even if this fixes your symptoms.<br>
<br>
</blockquote>
<br>
I figured as much, just thought I'd check to see if I'd missed anything obvious. Thanks for the reply. I'll file a bugzilla.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Mark<br>
> The coordinate file was then input into pdb2gmx with an<br>
> oplsaa.ff directory in the working directory. I received<br>
> the following error (identical with version 4.5 and the most<br>
> recent git with release-4-5-patches):<br>
><br>
> pdb2gmx -f struct.pdb<br>
> ...<br>
> -------------------------------------------------------<br>
> Program pdb2gmx, VERSION 4.5.1-20100920-03d181e<br>
> Source code file: pdb2gmx.c, line: 655<br>
><br>
> Fatal error:<br>
> Atom OXT in residue CRO 331 was not found in rtp entry CRO with<br>
> 39 atoms<br>
> while sorting atoms.<br>
> .<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/Documentation/Errors</a><br>
> -------------------------------------------------------<br>
><br>
> The CRO residue is my chromophore. I'm wondering why<br>
> pdb2gmx is finding an OXT atom in the following coordinates:<br>
><br>
> ...<br>
> ATOM 2528 N LEU A<br>
> 330 -13.640 10.888 -25.907 > 1.00 0.00<br>
> ATOM 2529 CA LEU A<br>
> 330 -12.513 11.013 -26.852 > 1.00 0.00<br>
> ATOM 2530 C LEU A<br>
> 330 -11.281 10.183 -26.416 > 1.00 0.00<br>
> ATOM 2531 O LEU A<br>
> 330 -10.625 9.588 -<br>
> 27.277 1.00 0.00<br>
> ATOM 2532 CB LEU A<br>
> 330 -12.159 12.493 -27.066 > 1.00 0.00<br>
> ATOM 2533 CG LEU A<br>
> 330 -13.206 13.415 -27.691 > 1.00 0.00<br>
> ATOM 2534 CD1 LEU A<br>
> 330 -12.913 14.905 -27.393 > 1.00 0.00<br>
> ATOM 2535 CD2 LEU A<br>
> 330 -13.400 13.160 -29.207 > 1.00 0.00<br>
> ATOM 2536 N CRO A<br>
> 331 -10.669 9.142 -<br>
> 25.611 1.00 0.00<br>
> ATOM 2537 CE CRO A<br>
> 331 -7.407 12.564 -<br>
> 27.240 1.00 0.00<br>
> ATOM 2538 SD CRO A<br>
> 331 -8.035 12.603 -<br>
> 25.595 1.00 0.00<br>
> ATOM 2539 CG1 CRO A<br>
> 331 -8.731 10.996 -<br>
> 25.519 1.00 0.00<br>
> ATOM 2540 CB1 CRO A<br>
> 331 -9.618 10.846 -<br>
> 24.279 1.00 0.00<br>
> ATOM 2541 CA1 CRO A<br>
> 331 -10.227 9.470 -<br>
> 24.406 1.00 0.00<br>
> ATOM 2542 C1 CRO A<br>
> 331 -10.304 8.516 -<br>
> 23.260 1.00 0.00<br>
> ATOM 2543 N2 CRO A<br>
> 331 -9.873 8.765 -<br>
> 21.981 1.00 0.00<br>
> ATOM 2544 OH CRO A<br>
> 331 -8.594 11.111 -<br>
> 15.969 1.00 0.00<br>
> ATOM 2545 CD2 CRO A<br>
> 331 -9.219 9.756 -<br>
> 19.205 1.00 0.00<br>
> ATOM 2546 CE2 CRO A<br>
> 331 -8.888 10.677 -<br>
> 18.207 1.00 0.00<br>
> ATOM 2547 CZ CRO A<br>
> 331 -8.898 10.286 -<br>
> 16.863 1.00 0.00<br>
> ATOM 2548 CE1 CRO A<br>
> 331 -9.219 8.975 -<br>
> 16.518 1.00 0.00<br>
> ATOM 2549 CD1 CRO A<br>
> 331 -9.549 8.056 -<br>
> 17.509 1.00 0.00<br>
> ATOM 2550 CG2 CRO A<br>
> 331 -9.557 8.447 -<br>
> 18.848 1.00 0.00<br>
> ATOM 2551 CB2 CRO A<br>
> 331 -9.880 7.417 -<br>
> 19.857 1.00 0.00<br>
> ATOM 2552 CA2 CRO A<br>
> 331 -10.149 7.645 -<br>
> 21.293 1.00 0.00<br>
> ATOM 2553 C2 CRO A<br>
> 331 -10.726 6.753 -<br>
> 22.143 1.00 0.00<br>
> ATOM 2554 O2 CRO A<br>
> 331 -11.108 5.574 -<br>
> 21.819 1.00 0.00<br>
> ATOM 2555 N3 CRO A<br>
> 331 -10.810 7.255 -<br>
> 23.355 1.00 0.00<br>
> ATOM 2556 CA3 CRO A<br>
> 331 -11.435 6.545 -<br>
> 24.488 1.00 0.00<br>
> ATOM 2557 C CRO A<br>
> 331 -10.492 6.111 -<br>
> 25.580 1.00 0.00<br>
> ATOM 2558 O CRO A<br>
> 331 -10.993 5.596 -<br>
> 26.570 1.00 0.00<br>
> ATOM 2559 N VAL A<br>
> 332 -9.265 5.813 -<br>
> 25.096 1.00 0.00<br>
> ATOM 2560 CA VAL A<br>
> 332 -8.235 4.899 -<br>
> 25.607 1.00 0.00<br>
> ATOM 2561 C VAL A<br>
> 332 -7.512 4.308 -<br>
> 24.397 1.00 0.00<br>
> ATOM 2562 O VAL A<br>
> 332 -6.351 4.567 -<br>
> 24.155 1.00 0.00<br>
> ATOM 2563 CB VAL A<br>
> 332 -7.312 5.633 -<br>
> 26.627 1.00 0.00<br>
> ATOM 2564 CG1 VAL A<br>
> 332 -8.127 5.980 -<br>
> 27.896 1.00 0.00<br>
> ATOM 2565 CG2 VAL A<br>
> 332 -6.687 6.887 -<br>
> 26.051 1.00 0.00<br>
> ...<br>
><br>
> Any ideas on what's going on? I can upload a bugzilla if<br>
> necessary, I just thought I'd report here first since I'm not<br>
> sure if I'm doing something wrong with respect to the many new<br>
> pdb2gmx features.<br>
><br>
> -Justin<br>
><br>
> --<br>
> ========================================<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> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
> --<br>
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</blockquote>
<br>
-- <br>
========================================<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> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Postdoctoral Research Scholar,<br>Department of Chemistry,<br>University of Nevada, Reno.<br>