Re: protonating ASP and GLU

From: Nehad Elsalamouny (
Date: Tue Dec 13 2016 - 12:48:35 CST

I am using amber force field so what will be the modified residue names in that case?


On Dec 14, 2016, at 1:27 AM, Brian Radak <<>> wrote:

This all depends on what force field you are using, since the modified residue names are non-PDB standard as far as I know.

For CHARMM36 the patches are ASPP and GLUP, so I would replace your mutate commands with the following:

patch GLUP xxxx:20 xxxx:25 xxxx:62
patch ASPP xxxx:65



On 12/13/2016 05:58 AM, Nehad Elsalamouny wrote:
Dear NAMD users,

I need to generate a psf file with protonated ASP and GLU residues using the following script:

package require psfgen
topology ../../xxxx.rtf
topology ../../xxxx.rtf
topology ../../xxxx.rtf

pdbalias atom ILE CD1 CD
pdbalias residue HIS HID

segment xxxx {
pdb xxxx.pdb
mutate 20 GLH
mutate 25 GLH
mutate 62A GLH
mutate 65 ASH
coordpdb xxxx.pdb xxxx
regenerate resids

patch DISU uPA:62 uPA:46
patch DISU uPA:125 uPA:54
patch DISU uPA:219 uPA:150
patch DISU uPA:198 uPA:182
patch DISU uPA:238 uPA:209

segment xxxx {first none; last none; auto none; pub xxxx.pdb}
coordpdb xxxx.pdb xxxx
segment xxxx {first none; last none; auto none; pdb xxxx.pdb}
coordpdb xxxx.pdb xxxx
segment xxxxx {first NONE; last NONE; auto none; pdb xxxxx.pdb}
coordpdb xxxxx.pdb xxxx

writepdb xxxxx.pdb
writepsf xxxxx.psf

The mutate command works well for for GLU and they are converted to GLH, however I receive an error message for ASP: unknown residue type ASH.
What is the problem? And how can I protonate the ASP?



Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643<>

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