From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Fri Jul 29 2011 - 03:16:50 CDT
Hi
Thanks for your help. I am going to try with it.
Hernán Andrés Morales Navarrete
Biophysics and Molecular Modeling Group
Physics Department
Escuela Politécnica Nacional, Quito - Ecuador
Ladrón de Guevara E11-253.
Casilla 17-01-1253
http://www.ciencias.epn.edu.ec/~biomod/
Date: Thu, 28 Jul 2011 12:15:52 +0530
Subject: Re: namd-l: DPPC membrane
From: ksubbu85_at_gmail.com
To: andresmoralesn2_at_hotmail.com
hi
the topology file topology top_all27_prot_lipid.rtf will work for protein with POPC bilayer only.the way you chosen is not correct for DPPC bilayer.
you have to options
1. if you want to study your peptide in any membrane then proceed with your peptide and POPC bilayer.
2.if you want to study your peptide in DPPC bilayer (other than POPC) only you need to build your own .pdb and .psf and parameter files
for this I used charmm-gui.it will build all files that needed to NAMD input file.
If you find any other way to build your system let me know
regards
subbarao kanchi.
iisc bangalore
india.
On Thu, Jul 28, 2011 at 11:59 AM, 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
resetpsf
package require psfgen
topology top_all27_prot_lipid.rtf
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.
Hernán Andrés Morales Navarrete
Biophysics and Molecular Modeling Group
Physics Department
Escuela Politécnica Nacional, Quito - Ecuador
Ladrón de Guevara E11-253.
Casilla 17-01-1253
http://www.ciencias.epn.edu.ec/~biomod/
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