From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
Date: Thu Jul 29 2021 - 11:57:11 CDT

Dear all,

I wanted to do a test run for the molecular dynamics simulation of an amino
acid (AA) using Drude polarizable force field (FF). I picked ASP AA (
ASP_autopsf.pdb
<https://urldefense.com/v3/__https://drive.google.com/file/d/1Z_yT2e2S_JV2cyofpiV619SRMzienhBI/view?usp=sharing__;!!DZ3fjg!pkmnx8MMSQVZbGMgKYBA30oNz_XvNguj_C-pS534IKz1JUV1-5NnRmyoR13rvAF0Ug$ >)
and used psfgen (vmd-1.9.4a51) to create ASP .psf and .pdb files compatible
with Drude FF. Initially, I performed the following script without the
terminal patches (first NTER; last CTER) and I noticed that some atoms
from the ASP terminals are missing. Then, I added the terminal patches as
follows, but the produced .pdb file ( ASP-p.pdb
<https://urldefense.com/v3/__https://drive.google.com/file/d/1NRrI727YXb_Xef4U-dS_RRIL0qD9A78g/view?usp=sharing__;!!DZ3fjg!pkmnx8MMSQVZbGMgKYBA30oNz_XvNguj_C-pS534IKz1JUV1-5NnRmyoR10JVpWmLg$ >
 & ASP-p.psf
<https://urldefense.com/v3/__https://drive.google.com/file/d/17B3HXdVhxuOeV94I8I03omjfS96jv46y/view?usp=sharing__;!!DZ3fjg!pkmnx8MMSQVZbGMgKYBA30oNz_XvNguj_C-pS534IKz1JUV1-5NnRmyoR139h5dn8Q$ >)
contains an extra Oxygen atom (and related lone-pair) located at the origin
which is far from the ASP itself.
############
package require psfgen
topology drude_toppar_2019/toppar_drude_master_protein_2019g.str
segment AP1 {
pdb ASP_autopsf.pdb
first NTER
last CTER
auto angles dihedrals
}
coordpdb ASP_autopsf.pdb AP1
guesscoord
writepdb ASP-p.pdb
<https://urldefense.com/v3/__https://drive.google.com/file/d/1NRrI727YXb_Xef4U-dS_RRIL0qD9A78g/view?usp=sharing__;!!DZ3fjg!pkmnx8MMSQVZbGMgKYBA30oNz_XvNguj_C-pS534IKz1JUV1-5NnRmyoR10JVpWmLg$ >
writepsf ASP-p.psf
<https://urldefense.com/v3/__https://drive.google.com/file/d/17B3HXdVhxuOeV94I8I03omjfS96jv46y/view?usp=sharing__;!!DZ3fjg!pkmnx8MMSQVZbGMgKYBA30oNz_XvNguj_C-pS534IKz1JUV1-5NnRmyoR139h5dn8Q$ >
######################

The relate lines of .pdb are as following:

###################
REMARK original generated coordinate pdb file
ATOM 1 N ASP A 201 54.031 29.991 188.076 1.00 0.00 AP1
 N
ATOM 2 DN ASP A 201 54.031 29.991 188.076 1.00 0.00 AP1
 N
ATOM 3 HT1 ASP A 201 54.797 30.563 188.371 1.00 0.00 AP1
 H
ATOM 4 HT2 ASP A 201 53.531 29.653 188.874 1.00 0.00 AP1
 H
ATOM 5 HT3 ASP A 201 53.418 30.519 187.488 1.00 0.00 AP1
 H
ATOM 6 CA ASP A 201 54.552 28.848 187.319 1.00 0.00 AP1
 C
ATOM 7 DCA ASP A 201 54.552 28.848 187.319 1.00 0.00 AP1
 C
ATOM 8 HA ASP A 201 55.030 29.254 186.434 1.00 0.00 AP1
 H
ATOM 9 C ASP A 201 53.431 27.920 186.831 1.00 0.00 AP1
 C
ATOM 10 DC ASP A 201 53.431 27.920 186.831 1.00 0.00 AP1
 C

*ATOM 11 O ASP A 201 0.000 0.000 0.000 -1.00 0.00
 AP1 OATOM 12 DO ASP A 201 0.000 0.000 0.000 -1.00 0.00
   AP1 OATOM 13 LPOA ASP A 201 0.000 0.000 0.000 -1.00 0.00
     AP1 HATOM 14 LPOB ASP A 201 0.000 0.000 0.000 -1.00
 0.00 AP1 H*
ATOM 15 OT1 ASP A 201 52.551 28.286 187.132 1.00 0.00 AP1
 O
ATOM 16 DOT1 ASP A 201 52.551 28.286 187.132 1.00 0.00 AP1
 O
ATOM 17 OT2 ASP A 201 53.836 27.160 186.323 1.00 0.00 AP1
 O
ATOM 18 DOT2 ASP A 201 53.836 27.160 186.323 1.00 0.00 AP1
 O
##################

Would you kindly guide me on what is wrong?

All the best,
Zeynab