AMBER Archive (2009)

Subject: RE: [AMBER] makeDIST_RST: no map function

From: Duggan, Brendan M. (bmduggan_at_musc.edu)
Date: Tue Sep 15 2009 - 08:40:00 CDT

In my email reader your mapping for residue MOL has asterisks (*) in the name "MOL" and around the first "MAPPING" label. If you have those in your file I think they should be removed.

In my map files the RESIDUE label is always in all caps, this too may be important.

brendan

email: bmduggan_at_musc.edu
phone: (843) 792 5029
fax: (843) 792 4322

________________________________________
From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of Workalemahu Berhanu [awberhanu_at_gmail.com]
Sent: Monday, September 14, 2009 3:30 PM
To: amber_at_ambermd.org
Subject: [AMBER] makeDIST_RST: no map function

Dear Amber users

I use makeDIST_RST to create *Distance restraints*. Since no standard map
file is provided for my organic molecule, I created one that maps all atoms
of the residues in a molecule and then I added at the end

Residue MO*L*

*MAPPING* O22 = O22

MAPPING H30 = H30

MAPPING C18 = C18

MAPPING C19 = C19

MAPPING H23 = H23

MAPPING C17 = C17

MAPPING O21 = O21

MAPPING H31 = H31

MAPPING C16 = C16

MAPPING O20 = O20

MAPPING H32 = H32

MAPPING C15 = C15

MAPPING H33 = H33

MAPPING C14 = C14

MAPPING C4 = C4

MAPPING O5 = O5

MAPPING C3 = C3

MAPPING O25 = O25

MAPPING H26 = H26

MAPPING C2 = C2

MAPPING O24 = O24

MAPPING C1 = C1

MAPPING C6 = C6

MAPPING C7 = C7

MAPPING H11 = H11

MAPPING C8 = C8

MAPPING O12 = O12

MAPPING H29 = H29

MAPPING C9 = C9

MAPPING H13 = H13

MAPPING C10 = C10

MAPPING O27 = O27

MAPPING H28 = H28

I use the 7-column format for the input file

20 ASN HD22 71 MOL H23 15.0

The following command gives error message:

makeDIST_RST -upb 7col1.dist -pdb GNNQQNYMYR_gb_min.pdb -rst RST.dist

# makeDIST_RST

Currently configured for up to 5000 atoms

Using MAP file /scratch2/ProjectData/usg/amber/10.0/dat/map.DG-AMBER

ERROR no map function for H23 MOL :data= 20 ASN HD22 71 MOL
H23
15.0

I checked in the atom names exist in the MOL and ASN
residues

I have attached the GNNQQNYMYR_gb_min.pdb

Thanks very much.

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