[gmx-users] bad bond in polymer
Justin A. Lemkul
jalemkul at vt.edu
Fri Aug 14 20:46:19 CEST 2009
The problem is in how you handle impropers. From your previous post, your [DRG]
entry had the following:
[ impropers ]
CAG CAF -CAM C
-CAM -CAN -CAI C
CAJ CAI OAL O
CAN CAM OAP O
CAI CAH CAJ C
The last column needs to correspond to an actual atom name; there may also be
issues with atom naming, since that previous post also had different atom names
for DR0, DRG, and DR1 residues. In the attached .pdb file, you appear to have
uniform naming between all of the residues.
Be careful which files you are using; it looks like you have made multiple
attempts. If things still aren't working out, please post:
1. The error message you are getting.
2. The .pdb file.
3. The current .rtp entries.
-Justin
nicegromacs wrote:
> Hi Justin,
>
> ups!! I am sorry this is the exact .pdb file.
>
> HETATM 1 CAA DR0 1 83.043 46.127 36.820 1.00 0.00
> HETATM 2 CAB DR0 1 82.411 45.765 35.421 1.00 0.00
> HETATM 3 CAC DR0 1 81.495 46.822 34.598 1.00 0.00
> HETATM 4 CAD DR0 1 80.621 46.369 33.071 1.00 0.00
> HETATM 5 CAE DR0 1 79.305 47.302 32.172 1.00 0.00
> HETATM 6 CAF DR0 1 77.939 46.749 31.124 1.00 0.00
> HETATM 7 CAG DR0 1 76.264 47.439 30.612 1.00 0.00
> HETATM 8 CAH DR0 1 74.636 46.805 29.962 1.00 0.00
> HETATM 9 CAI DR0 1 72.805 47.674 30.179 1.00 0.00
> HETATM 10 CAJ DR0 1 73.794 48.838 31.123 1.00 0.00
> HETATM 11 OAK DR0 1 74.815 49.342 30.292 1.00 0.00
> HETATM 12 OAL DR0 1 74.592 48.143 32.194 1.00 0.00
> HETATM 13 CAM DR0 1 71.093 47.685 29.486 1.00 0.00
> HETATM 14 CAN DR0 1 71.598 47.212 28.208 1.00 0.00
> HETATM 15 OAO DR0 1 72.440 48.255 27.735 1.00 0.00
> HETATM 16 OAP DR0 1 72.374 46.050 28.399 1.00 0.00
> HETATM 17 CAA DRG 2 72.093 46.197 36.714 1.00 0.00
> HETATM 18 CAB DRG 2 71.418 45.759 35.400 1.00 0.00
> HETATM 19 CAC DRG 2 71.084 46.901 34.417 1.00 0.00
> HETATM 20 CAD DRG 2 70.620 46.251 33.139 1.00 0.00
> HETATM 21 CAE DRG 2 70.650 47.255 32.000 1.00 0.00
> HETATM 22 CAF DRG 2 69.655 46.512 30.955 1.00 0.00
> HETATM 23 CAG DRG 2 69.081 47.504 29.843 1.00 0.00
> HETATM 24 CAH DRG 2 67.208 47.518 29.256 1.00 0.00
> HETATM 25 CAI DRG 2 65.298 47.601 29.691 1.00 0.00
> HETATM 26 CAJ DRG 2 65.629 48.362 30.827 1.00 0.00
> HETATM 27 OAK DRG 2 65.140 49.590 30.429 1.00 0.00
> HETATM 28 OAL DRG 2 64.837 47.815 31.709 1.00 0.00
> HETATM 29 CAM DRG 2 63.041 47.557 29.333 1.00 0.00
> HETATM 30 CAN DRG 2 62.808 47.023 27.931 1.00 0.00
> HETATM 31 OAO DRG 2 63.130 48.142 27.185 1.00 0.00
> HETATM 32 OAP DRG 2 63.560 45.894 27.706 1.00 0.00
> HETATM 33 CAA DRG 3 61.174 46.188 36.668 1.00 0.00
> HETATM 34 CAB DRG 3 60.510 45.777 35.344 1.00 0.00
> HETATM 35 CAC DRG 3 60.221 46.928 34.352 1.00 0.00
> HETATM 36 CAD DRG 3 59.724 46.337 32.998 1.00 0.00
> HETATM 37 CAE DRG 3 60.252 47.307 31.985 1.00 0.00
> HETATM 38 CAF DRG 3 61.089 46.606 30.881 1.00 0.00
> HETATM 39 CAG DRG 3 60.868 47.564 29.740 1.00 0.00
> HETATM 40 CAH DRG 3 58.621 47.652 29.253 1.00 0.00
> HETATM 41 CAI DRG 3 56.328 47.703 29.755 1.00 0.00
> HETATM 42 CAJ DRG 3 55.914 48.516 30.963 1.00 0.00
> HETATM 43 OAK DRG 3 55.050 49.545 30.403 1.00 0.00
> HETATM 44 OAL DRG 3 54.945 47.724 31.565 1.00 0.00
> HETATM 45 CAM DRG 3 54.420 47.478 29.367 1.00 0.00
> HETATM 46 CAN DRG 3 53.587 47.142 27.983 1.00 0.00
> HETATM 47 OAO DRG 3 52.713 48.009 27.325 1.00 0.00
> HETATM 48 OAP DRG 3 53.396 45.805 27.517 1.00 0.00
> HETATM 49 CAA DR1 4 50.257 46.173 36.646 1.00 0.00
> HETATM 50 CAB DR1 4 49.673 45.778 35.270 1.00 0.00
> HETATM 51 CAC DR1 4 49.360 46.939 34.273 1.00 0.00
> HETATM 52 CAD DR1 4 49.270 46.480 32.735 1.00 0.00
> HETATM 53 CAE DR1 4 50.289 47.086 31.602 1.00 0.00
> HETATM 54 CAF DR1 4 51.813 46.713 31.234 1.00 0.00
> HETATM 55 CAG DR1 4 52.487 47.720 29.966 1.00 0.00
> HETATM 56 CAH DR1 4 50.870 47.989 29.178 1.00 0.00
> HETATM 57 CAI DR1 4 48.982 47.816 29.191 1.00 0.00
> HETATM 58 CAJ DR1 4 47.901 48.319 30.192 1.00 0.00
> HETATM 59 OAK DR1 4 47.004 49.132 29.503 1.00 0.00
> HETATM 60 OAL DR1 4 46.963 47.171 30.588 1.00 0.00
> HETATM 61 CAM DR1 4 47.752 46.922 28.157 1.00 0.00
> HETATM 62 CAN DR1 4 46.372 47.149 27.020 1.00 0.00
> HETATM 63 OAO DR1 4 45.018 47.950 26.877 1.00 0.00
> HETATM 64 OAP DR1 4 46.019 46.082 26.137 1.00 0.00
> TER
> ENDMDL
>
>
> --------------------------------------------------
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Sent: Friday, August 14, 2009 12:14 PM
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] bad bond in polymer
>
>>
>>
>> nicegromacs wrote:
>>> I follow some of the step of
>>> http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
>>> (I omitted the change in the .hdb file because I don't have explicit
>>> hydrogens). Well, I build a polymer with 3 units. The head (H), one
>>> repeat unit (R)and tail (T) for the polymer (H-R-T) and this gives
>>> ok, but when I add one more repetitive unit (H-R-R-T) I get the
>>> following error:
>>> Program pdb2gmx, VERSION 3.3.3
>>> Source code file: ../../../../src/kernel/pgutil.c, line: 87
>>> Fatal error:
>>> Atom CAM not found in residue 1083339441 while adding improper
>>>
>>> -------------------------------------------------------
>>>
>>
>> It looks like pdb2gmx is finding some kind of undefined residue. Can
>> you post the .pdb file?
>>
>> -Justin
>>
>>> "Stop Drinking My Beer !" (The Amps)
>>>
>>>
>>>>
>>>>
>>>> nicegromacs wrote:
>>>>
>>>>> CAG -CAM
>>>>
>>>> Defining a bond to a previous residue will certainly fail for at
>>>> least one terminus of your polymer chain. You may find this post
>>>> useful:
>>>>
>>>> http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html
>>>>
>>>> If things still aren't working, please post the structure file, as
>>>> well, and identify the bond that is being formed that shouldn't.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>> _______________________________________________
>>>> gmx-users mailing list gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at http://www.gromacs.org/search before
>>>> posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>>
>>>
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list