Re: DPPC membrane

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Jul 28 2011 - 05:21:10 CDT

Hi,

This might not help you directly, but have you tried using CHARMM-GUI. It
has worked very well for me so far. Also there is a never version of the
CHARMM force field for lipids that fixes the area per lipid problem in the
old versions [1].

Regarding your original problem: The topology file that you're loading with
the line

 topology top_all27_prot_lipid.rtf

does not contain a residue named DPP, which is why psfgen complains.
You have to load the topology file that came with the package downloaded
from lipidbook.

Best regards,
Ajasja

1: Jeffery B. Klauda et al., Update of the CHARMM All-Atom Additive Force
Field for Lipids: Validation on Six Lipid Types, The Journal of Physical
Chemistry B 114, no. 23 (June 17, 2010): 7830-7843.

On Thu, Jul 28, 2011 at 08:29, Andres Morales N <andresmoralesn2_at_hotmail.com
> wrote:

> Dear NAMD Users:
>
>
> I am trying to run a simulation of DPPC lipid bilayer with a cationic
> peptide.
>
> I got a DPPC pre equilibrated membrane from LIPIDBOOK (
> http://lipidbook.bioch.ox.ac.uk). I want to run my simulations using that
> pdb file.
> I tried to get the corresponding pdf file using AUTOMATIC PSF BULIDER from
> VMD, but there is a problem with some residues:
> "unknown residue type SOL
> unknown residue type DPPC"
> I also tried using the following TCL script:
>
>
> set membrana [mol load pdb membrana.pdb]
> set mem [atomselect $membrana all]
> $mem writepdb mem_1.pdb
> topology top_all27_prot_lipid.rtf
> package require psfgen
> topology
> segment U {pdb mem_1.pdb}
> pdbalias residue HOH TIP3
> pdbalias atom ILE CD1 CD
> coordpdb mem_1.pdb U
> guesscoord
> writepdb dppc.pdb
> writepsf dppc.psf
>
> And I had the same problem:
>
> "unknown residue type SOL
> extracted 5969 residues from pdb file
> Info: generating structure...
> unknown residue type DPP
> ERROR: failed on end of segment
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over."
>
> The original pdf file is:
>
>
> HEADER Equilibrated 128-DPPC bilayer (t=190ns)
> REMARK Hydrated bilayer (5841 H2Os)
> JRNL AUTH D. POGER, W.F. VAN GUNSTEREN, A.E. MARK
> JRNL REF J. COMPUT. CHEM. DOI: 10.1002/jcc.21396
> CRYST1 63.398 63.398 83.985 90.00 90.00 90.00 P 1 1
> MODEL 1
> ATOM 1 CN1 DPP 1 2.181 26.328 -1.989 1.00 0.00
> ATOM 2 CN2 DPP 1 3.881 25.588 -0.379 1.00 0.00
> ATOM 3 CN3 DPP 1 3.811 24.758 -2.639 1.00 0.00
> ATOM 4 NTM DPP 1 3.571 25.928 -1.779 1.00 0.00
> ATOM 5 CA DPP 1 4.391 27.058 -2.219 1.00 0.00
> ATOM 6 CB DPP 1 4.631 28.268 -1.309 1.00 0.00
> ATOM 7 OA DPP 1 3.411 29.018 -1.219 1.00 0.00
> ATOM 8 P DPP 1 3.411 29.608 0.281 1.00 0.00
> ATOM 9 OB DPP 1 4.731 29.948 0.861 1.00 0.00
> ATOM 10 OC DPP 1 2.201 30.468 0.351 1.00 0.00
> ATOM 11 OD DPP 1 2.811 28.318 1.031 1.00 0.00
> ATOM 12 CC DPP 1 2.451 28.698 2.361 1.00 0.00
> ATOM 13 CD DPP 1 1.571 27.668 3.061 1.00 0.00
> ATOM 14 OE DPP 1 0.851 28.188 4.181 1.00 0.00
> ATOM 15 C1A DPP 1 -0.469 28.058 4.281 1.00 0.00
> ATOM 16 OF DPP 1 -1.149 27.598 3.361 1.00 0.00
> ATOM 17 C1B DPP 1 -0.979 28.648 5.531 1.00 0.00
> ATOM 18 C1C DPP 1 -1.889 27.598 6.191 1.00 0.00
> ATOM 19 C1D DPP 1 -1.029 26.478 6.781 1.00 0.00
> ATOM 20 C1E DPP 1 -1.569 25.858 8.071 1.00 0.00
> ATOM 21 C1F DPP 1 -0.419 25.158 8.801 1.00 0.00
> ATOM 22 C1G DPP 1 -0.359 25.578 10.271 1.00 0.00
> ATOM 23 C1H DPP 1 0.641 24.728 11.061 1.00 0.00
> ATOM 24 C1I DPP 1 0.481 25.048 12.541 1.00 0.00
> ATOM 25 C1J DPP 1 1.281 24.208 13.531 1.00 0.00
> ATOM 26 C1K DPP 1 1.321 22.678 13.511 1.00 0.00
> ATOM 27 C1L DPP 1 2.541 22.068 14.201 1.00 0.00
> ATOM 28 C1M DPP 1 2.771 20.708 13.541 1.00 0.00
> ATOM 29 C1N DPP 1 3.191 20.838 12.071 1.00 0.00
> ATOM 30 C1O DPP 1 4.471 21.578 11.681 1.00 0.00
> ATOM 31 C1P DPP 1 4.451 21.958 10.201 1.00 0.00
> ATOM 32 CE DPP 1 2.381 26.378 3.211 1.00 0.00
> ATOM 33 OG DPP 1 3.471 26.578 4.121 1.00 0.00
> ATOM 34 C2A DPP 1 4.281 25.528 4.221 1.00 0.00
> ATOM 35 OH DPP 1 4.211 24.498 3.541 1.00 0.00
> ATOM 36 C2B DPP 1 5.291 25.568 5.301 1.00 0.00
> ATOM 37 C2C DPP 1 4.681 25.128 6.631 1.00 0.00
> ATOM 38 C2D DPP 1 5.611 25.388 7.811 1.00 0.00
> ATOM 39 C2E DPP 1 4.891 25.658 9.141 1.00 0.00
> ATOM 40 C2F DPP 1 6.141 25.858 9.991 1.00 0.00
> ATOM 41 C2G DPP 1 5.811 26.178 11.451 1.00 0.00
> ATOM 42 C2H DPP 1 6.961 26.458 12.411 1.00 0.00
> ATOM 43 C2I DPP 1 6.491 26.918 13.801 1.00 0.00
> ATOM 44 C2J DPP 1 5.651 25.878 14.521 1.00 0.00
> ATOM 45 C2K DPP 1 4.631 26.448 15.511 1.00 0.00
> ATOM 46 C2L DPP 1 3.901 25.428 16.391 1.00 0.00
> ATOM 47 C2M DPP 1 4.761 24.678 17.411 1.00 0.00
> ATOM 48 C2N DPP 1 4.031 23.988 18.561 1.00 0.00
> ATOM 49 C2O DPP 1 3.161 22.818 18.091 1.00 0.00
> ATOM 50 C2P DPP 1 2.671 21.988 19.271 1.00 0.00
> ATOM 51 CN1 DPP 2 12.691 12.778 35.801 1.00 0.00
> .....
> ATOM 6401 OW SOL 129 31.131 5.048 76.381 1.00 0.00
> ATOM 6402 HW1 SOL 129 30.901 4.848 75.431 1.00 0.00
> ATOM 6403 HW2 SOL 129 30.601 5.838 76.701 1.00 0.00
> ATOM 6404 OW SOL 130 43.741 9.588 60.861 1.00 0.00
> ATOM 6405 HW1 SOL 130 44.171 10.468 61.091 1.00 0.00
> ATOM 6406 HW2 SOL 130 43.681 9.498 59.871 1.00 0.00
> ATOM 6407 OW SOL 131 37.711 49.268 31.401 1.00 0.00
> ATOM 6408 HW1 SOL 131 37.671 49.498 30.431 1.00 0.00
> ATOM 6409 HW2 SOL 131 36.861 49.538 31.841 1.00 0.00
> ATOM 6410 OW SOL 132 48.781 5.928 46.911 1.00 0.00
> ATOM 6411 HW1 SOL 132 48.541 5.078 46.441 1.00 0.00
> ATOM 6412 HW2 SOL 132 48.011 6.558 46.881 1.00 0.00
> ATOM 6413 OW SOL 133 41.711 61.788 60.611 1.00 0.00
> ATOM 6414 HW1 SOL 133 40.911 61.338 60.201 1.00 0.00
> ATOM 6415 HW2 SOL 133 41.441 62.218 61.481 1.00 0.00
> ....
> TER
> ENDMDL
>
>
> Does anybody know how to solve it?
>
>
> I wait that someone can help me with this.
>
>
>
> Thanks for your help.
>
>
>
>
>
>
>
> Hernn Andrs Morales Navarrete
>
> Biophysics and Molecular Modeling Group
> Physics Department
> Escuela Politcnica Nacional, Quito - Ecuador
> Ladrn de Guevara E11-253.
> Casilla 17-01-1253
> http://www.ciencias.epn.edu.ec/~biomod/
>
>
>
>

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