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#468 10/29/03 08:50 PM
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cao Offline OP
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Dear all,

I just do some simple things:
open top_all22_prot.inp
read rtf
open par_all22_prot.inp
read para
open
open unit 12 read form name "@TOPPAR/par_hbond.inp"
read param card unit 12 append

Then, I got the following warnings:

PARRDR> WARNING: ATOMS IN HBOND N N%%% -5.00000 3.00000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND N% N%%% -5.00000 3.00000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND N%% N%%% -5.00000 3.00000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND N%%% N -5.00000 3.00000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND N%%% N% -5.00000 3.00000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND N%%% N%% -5.00000 3.00000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND N%%% N%%% -5.00000 3.00000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND N O%%% -4.90000 2.90000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND N% O%%% -4.90000 2.90000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND N%% O%%% -4.90000 2.90000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND N%%% O -4.90000 2.90000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND N%%% O% -4.90000 2.90000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND N%%% O%% -4.90000 2.90000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND N%%% O%%% -4.90000 2.90000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND O N%%% -4.85000 2.85000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND O% N%%% -4.85000 2.85000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND O%% N%%% -4.85000 2.85000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND O%%% N -4.85000 2.85000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND O%%% N% -4.85000 2.85000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND O%%% N%% -4.85000 2.85000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND O%%% N%%% -4.85000 2.85000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND O O%%% -4.75000 2.75000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND O% O%%% -4.75000 2.75000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND O%% O%%% -4.75000 2.75000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND O%%% O -4.75000 2.75000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND O%%% O% -4.75000 2.75000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND O%%% O%% -4.75000 2.75000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND O%%% O%%% -4.75000 2.75000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND S N%%% -3.50000 3.00000 DONT EXIST
PARRDR> WARNING: ATOMS IN HBOND S O%%% -3.50000 2.90000 DONT EXIST
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.

The version is c29b2.
What do those warning mean? Any tips of improving them? Will it hurt my analysis of hbond later?

Thanks in advance!

cao #469 10/29/03 10:18 PM
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You probably want to analyze hydrogen bonds in your system. Current parametrizations of the energy function in CHARMM do not use an explicit hydrogen bond term (even though it is supported by the program); the file par_hbond.inp contains more warnings than actual data!
Your best option is to use the COOR HBONd command (corman.doc) as exemplified by hbonds.inp in the Script Archive forum. This command alllows analysis of direct or water mediated hbonds (based on geometric criteria) from single structures or trajectories, including time dependent properties; an energetic analysis may still be performed using the INTEraction_energy command, which is consistent with the energy function used in generating the structure.



Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
cao #470 10/30/03 03:34 AM
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rmv Online Content
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The warnings are harmless and can be ignored; they will not affect any subsequent analysis. The par_hbond.inp file was designed to be used for HBOND analysis with virtually any existing CHARMM parameter files, and over specifies the range of atom parameter types. It is required for use with listing commands such as

PRINT HBOND ANAL

or for examining a specific H-bond in detail as an H-bond energy time series in CORREL. These methods are complementary to COOR HBOND, and it's quite useful to run more than one method of analysis.


Rick Venable
computational chemist

rmv #471 10/30/03 03:59 AM
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cao Offline OP
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Thanks for Rick's and Lennart's responses!
Now I am not worry about the warnings any more.

BTW: I found, when I read top_all27_prot_na.rtf and par_all27_prot_na.prm, no any warnings at all.


Moderated by  lennart, rmv 

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