From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Fri Mar 17 2017 - 05:03:42 CDT
Hello,
I can't be 100% certain but I think the LPS files require the standard
charmm lipid topology (top_all36_lipid.rtf) to function properly, since
the atoms of the hydrophobic tails are described there (this makes sense
since the Lipid A topology was modeled after DMPC). Try including that
in your psfgen script. You may also need to load the CGenFF files too.
Hope this helps,
Fotis
On 03/17/2017 06:19 AM, 송연호 wrote:
> Dear all.
>
> Hi all,
> I want to generate psf file for lipopolysaccharide(LPS) bilayer using
> psfgen.
> But, error has occured. I don't know how to solve this problem.
>
> ERROR
>
> in pdb file.-------------------------------------
>
> ATOM 83 H88R ECLI 1 -1.724 4.739 3.212 1.00 0.00
> LPS H
> ATOM 84 H88S ECLI 1 -3.499 5.177 3.706 1.00 0.00
> LPS H
> ATOM 85 C89 ECLI 1 -3.062 3.087 3.350 1.00 0.00
> LPS C
> ATOM 86 H89R ECLI 1 -2.326 2.294 3.471 1.00 0.00
> LPS H
> ATOM 87 H89S ECLI 1 -3.266 3.193 2.213 1.00 0.00
> LPS H
> ATOM 88 C810 ECLI 1 -4.459 2.542 3.852 1.00 0.00
> LPS C
> ATOM 89 H810 ECLI 1 -5.289 3.323 3.694 1.00 0.00
> LPS H
> ATOM 90 H810 ECLI 1 -4.302 2.443 4.903 1.00 0.00
> LPS H
> ATOM 91 C811 ECLI 1 -4.686 1.225 3.095 1.00 0.00
> LPS C
> ATOM 92 H811 ECLI 1 -3.874 0.518 3.435 1.00 0.00
> LPS H
> ATOM 93 H811 ECLI 1 -4.558 1.368 1.977 1.00 0.00
> LPS H
> ATOM 94 C812 ECLI 1 -6.032 0.663 3.552 1.00 0.00
> LPS C
> ATOM 95 H812 ECLI 1 -6.782 1.442 3.616 1.00 0.00
> LPS H
> ATOM 96 H812 ECLI 1 -5.943 0.264 4.590 1.00 0.00
> LPS H
> ATOM 97 C813 ECLI 1 -6.411 -0.574 2.795 1.00 0.00
> LPS C
> ATOM 98 H813 ECLI 1 -5.671 -1.399 2.978 1.00 0.00
> LPS H
> ATOM 99 H813 ECLI 1 -7.378 -0.969 3.103 1.00 0.00
> LPS H
> ATOM 100 C814 ECLI 1 -6.620 -0.398 1.260 1.00 0.00
> LPS C
> ATOM 101 H814 ECLI 1 -7.294 0.529 1.270 1.00 0.00
> LPS H
> ATOM 102 H814 ECLI 1 -7.219 -1.231 0.892 1.00 0.00
> LPS H
> ATOM 103 H814 ECLI 1 -5.659 -0.280 0.690 1.00 0.00
> LPS H
> ATOM 104 C74 ECLI 1 2.791 4.292 11.789 1.00 0.00
> LPS C
> ATOM 105 H74R ECLI 1 2.048 3.535 11.549 1.00 0.00
> LPS H
>
> in topology file.----------------------------------
>
> GROUP ! | | | | |
> ATOM C89 CTL2 -0.18 ! | | |
> ATOM H89R HAL2 0.09 ! | | | | |
> ATOM H89S HAL2 0.09 ! H810R---C810---H810S H713R---C713---H713S |
> | |
> GROUP ! | | | | |
> ATOM C810 CTL2 -0.18 ! | | |
> ATOM H810R HAL2 0.09 ! | | | | |
> ATOM H810S HAL2 0.09 ! H811R---C811---H811S H714R---C714---H714S |
> | |
> GROUP ! | | | | |
> ATOM C811 CTL2 -0.18 ! H714T | | |
> ATOM H811R HAL2 0.09 ! | | | |
> ATOM H811S HAL2 0.09 ! H812R---C812---H812S | | |
> GROUP ! | | | |
> ATOM C812 CTL2 -0.18 ! | | |
> ATOM H812R HAL2 0.09 ! | | | |
> ATOM H812S HAL2 0.09 ! H813R---C813---H813S | | |
> GROUP ! | | | |
> ATOM C813 CTL2 -0.18 ! | | |
> ATOM H813R HAL2 0.09 ! | | | |
> ATOM H813S HAL2 0.09 ! H814R---C814---H814S | | |
> GROUP ! | | | |
> ATOM C814 CTL3 -0.27 ! H814S | | |
> ATOM H814R HAL3 0.09 ! | | |
> ATOM H814S HAL3 0.09 ! | | |
> ATOM H814T HAL3 0.09 ! | | |
> GROUP ! CHAIN 5 ! | | |
> ATOM C74 CTL2 -0.18 !
> ATOM H74R HAL2 0.09 ! | | |
> ATOM H74S HAL2 0.09 !
>
>
> in psfgen ---------------------------------------
>
> topology
> /home1/yeonho/research/CHARMM_FF/toppar/toppar_all36_lipid_lps.str
> topology
> /home1/yeonho/research/CHARMM_FF/toppar/toppar_all36_carb_imlab.str
> topology /home1/yeonho/research/CHARMM_FF/toppar/top_all36_carb.rtf
>
> segment LPS {
> pdbalias residue ECLI ECLIPA
> pdb ../../LPS_im_lipidA_Core/lps_modeler.yeonho.pdb
> pdbalias atom ECLI H814 H814R
> pdbalias atom ECLI H814 H814S
> pdbalias atom ECLI H814 H814T
> }
>
> writemol pdb lps_modeler.namd.pdb
> writemol psf lps_modeler.namd.psf
>
> psfgen error-------------------------------------
>
> psfgen) Created by CHARMM version 32 1
> psfgen) ERROR! Failed to parse autogenerate statement.
> psfgen) building segment LPS
> psfgen) aliasing residue ECLI to ECLIPA
> psfgen) reading residues from pdb file
> ../../LPS_im_lipidA_Core/lps_modeler.pdb
> psfgen) extracted 11 residues from pdb file
> psfgen) aliasing residue ECLI atom H814 to H814R
> psfgen) aliasing residue ECLI atom H814 to H814S
> psfgen) aliasing residue ECLI atom H814 to H814T
> psfgen) Info: generating structure...psfgen) unknown atom type HAL3
> psfgen) add atom failed in residue ECLIPA:1
> failed!
>
> --------------------------------------------------
>
> Please teach me to fix a problem and to generate PSF file using psfgen
> program.
>
> Thanks all.
>
> Yeonho Song.
-- ******************************************* Fotis A. Baltoumas Phd Candidate, Bioinformatics Postgraduate Programme Department of Cell Biology and Biophysics Faculty of Biology, University of Athens Panepistimiopolis, Athens 157 01, GREECE -------------------------------------- email : fbaltoumas_at_biol.uoa.gr http://biophysics.biol.uoa.gr http://bioinformatics.biol.uoa.gr *******************************************
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