problem to generate LPS PSF file using PSFGEN

From: 송연호 (syh6076_at_gmail.com)
Date: Thu Mar 16 2017 - 23:19:36 CDT

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.

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