VMD-L Mailing List

From: Daniela Rivas (dani.rivas.r_at_gmail.com)
Date: Wed Mar 08 2017 - 18:14:18 CST

Hi Joshua,

Here is the complete script that I used:

package require psfgen

topology top_all36_prot.rtf
topology top_all36_carb.rtf

pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD

segment P1 {
pdb P1.pdb
first NTER
last CTER
}

segment P2 {
pdb P2.pdb
first NTER
last CTER
}

patch DISU P1:109 P2:439
patch DISU P1:112 P2:442
patch DISU P1:144 P1:204
patch DISU P1:250 P1:308
patch DISU P2:474 P2:534
patch DISU P2:580 P2:638

coordpdb P1.pdb P1
coordpdb P2.pdb P2

pdbalias residue NAG AGLCNA
segment O1 {
pdb S1.pdb
}

coordpdb S1.pdb O1

pdbalias residue NAG BGLCNA
segment O2 {
pdb S2.pdb
}

coordpdb S2.pdb O2

segment O3 {
pdb S3.pdb
}

coordpdb S3.pdb O3

segment O4 {
pdb S4.pdb
}

coordpdb S4.pdb O4

pdbalias residue NAG BGLCNA
segment O5 {
pdb S5.pdb
}

coordpdb S5.pdb O5

segment O6 {
pdb S6.pdb
}

coordpdb S6.pdb O6

segment O7 {
pdb S7.pdb
}

coordpdb S7.pdb O7

pdbalias residue NAG BGLCNA
segment O8 {
pdb S8.pdb
}

coordpdb S8.pdb O8

segment O9 {
pdb S9.pdb
}

coordpdb S9.pdb O9

pdbalias residue NAG AGLCNA
segment O10 {
pdb SS1.pdb
}

coordpdb SS1.pdb O10

pdbalias residue NAG BGLCNA
segment O11 {
pdb SS2.pdb
}

coordpdb SS2.pdb O11

segment O12 {
pdb SS3.pdb
}

coordpdb SS3.pdb O12

segment O13 {
pdb SS4.pdb
}

coordpdb SS4.pdb O13

pdbalias residue NAG BGLCNA
segment O14 {
pdb SS5.pdb
}

coordpdb SS5.pdb O14

segment O15 {
pdb SS6.pdb
}

coordpdb SS6.pdb O15

pdbalias residue NAG BGLCNA
segment O16 {
pdb SS7.pdb
}

coordpdb SS7.pdb O16

segment O17 {
pdb SS8.pdb
}

coordpdb SS8.pdb O17

segment O18 {
pdb SS9.pdb
}

coordpdb SS9.pdb O18

guesscoord

writepdb IGG_Fc_psf.pdb
writepsf IGG_Fc_psf.psf

On 9 March 2017 at 02:54, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov> wrote:

> Hi Daniela,
>
> Could you paste in the rest of your script? The patch command looks right
> (assuming the segnames/resids are correct), so assuming you write out your
> pdb/psf pair afterward and load them in, the bond should totally exist.
>
> -Josh
>
> On 03/07/2017 08:33 PM, Daniela Rivas wrote:
> Hi all,
>
> I have generated the PSF file for my system, patching the N-glycosylation
> as follows:
>
> patch NGLB P1:180 O1:331
>
> Where P1 is my protein and O1 is the sugar.
>
> My script for building the PSF runs perfectly with no errors, but when I
> open the new PSF and PDB files I cannot see the bond between the protein
> and the sugar. I noticed that the correct Hydrogen and Oxygen atoms have
> been deleted, but somehow the bond is not there.
>
> Has anyone else have an issue like this before? Am I missing something?
>
> Cheers,
> Daniela.
>
>