Hello,
Since all the comments are for the parameters involving the DU atom type, I suspect that there is no DU atom type in the AMBER/GAFF force fields or you did not define this atom type. So check carefully your input files
Stef
________________________________________
De : shahab shariati [shahab.shariati.gmail.com]
Envoyé : vendredi 16 septembre 2016 20:25
À : amber
Objet : [AMBER] "ATTN, need revision" in frcmod file / Could not find bond parameter & Could not find angle parameter
Dear David,
Thanks for your guidance.
My problem was solved by changing "0" to "7" in "addions comp_sol Na+ 0".
But I have another problem about my another ligand, Paclitaxel(taxol).
I used 2 following command in AMBERTOOLS 14:
$AMBERHOME/bin/antechamber -i lig.pdb -fi pdb -o lig.mol2 -fo mol2 -c bcc
-s 2
$AMBERHOME/bin/parmchk -i lig.mol2 -f mol2 -o lig.frcmod
lig.pdb file:
https://cp.sync.com/dl/1fbba13a0#dq79chn2-7y5wnc8m-cpvadf4k-qzcjyu9e
lig.mol2 file:
https://cp.sync.com/dl/50079a740#dckrc4id-zx548z5k-juh4wzz6-da6zeb9n
and lig.frcmod file is as follows:
remark goes here
MASS
DU 0.000 0.000 ATTN, need revision
BOND
DU-ha 0.00 0.000 ATTN, need revision
DU-c3 0.00 0.000 ATTN, need revision
DU-DU 0.00 0.000 ATTN, need revision
ANGLE
c3-c3-DU 0.000 0.000 ATTN, need revision
DU-c3-DU 0.000 0.000 ATTN, need revision
DU-DU-c3 0.000 0.000 ATTN, need revision
DU-c3-c2 0.000 0.000 ATTN, need revision
DU-c3-h1 0.000 0.000 ATTN, need revision
DU-c3-os 0.000 0.000 ATTN, need revision
ha-DU-c3 0.000 0.000 ATTN, need revision
ha-DU-DU 0.000 0.000 ATTN, need revision
c3-DU-c3 0.000 0.000 ATTN, need revision
ca-c2-n 67.297 115.555 Calculated with empirical approach
ca-c2-o 69.801 119.785 Calculated with empirical approach
ca-c2-os 68.329 116.840 Calculated with empirical approach
cy-os-c2 67.090 103.270 Calculated with empirical approach
n -c2-o 74.833 117.460 Calculated with empirical approach
o -c2-os 76.640 118.745 Calculated with empirical approach
DIHE
c3-c3-DU-ha 1 0.000 0.000 0.000 ATTN, need
revision
c3-c3-DU-c3 1 0.000 0.000 0.000 ATTN, need
revision
c3-c3-DU-DU 1 0.000 0.000 0.000 ATTN, need
revision
DU-c3-DU-DU 1 0.000 0.000 0.000 ATTN, need
revision
ha-DU-c3-DU 1 0.000 0.000 0.000 ATTN, need
revision
ha-DU-DU-c3 1 0.000 0.000 0.000 ATTN, need
revision
ha-DU-c3-c2 1 0.000 0.000 0.000 ATTN, need
revision
ha-DU-c3-h1 1 0.000 0.000 0.000 ATTN, need
revision
ha-DU-c3-os 1 0.000 0.000 0.000 ATTN, need
revision
c3-DU-DU-c3 1 0.000 0.000 0.000 ATTN, need
revision
c3-DU-c3-c2 1 0.000 0.000 0.000 ATTN, need
revision
c3-DU-c3-h1 1 0.000 0.000 0.000 ATTN, need
revision
c3-DU-c3-os 1 0.000 0.000 0.000 ATTN, need
revision
DU-DU-c3-c2 1 0.000 0.000 0.000 ATTN, need
revision
DU-DU-c3-h1 1 0.000 0.000 0.000 ATTN, need
revision
DU-DU-c3-os 1 0.000 0.000 0.000 ATTN, need
revision
DU-c3-DU-c3 1 0.000 0.000 0.000 ATTN, need
revision
c3-cy-os-cy 1 0.383 0.000 3.000 same as X
-c3-os-X
hc-c3-cy-cy 1 0.156 0.000 3.000 same as X
-c3-c3-X
hc-c3-cy-h1 1 0.156 0.000 3.000 same as X
-c3-c3-X
hc-c3-cy-os 1 0.000 0.000 -3.000 same as
hc-c3-c3-os
hc-c3-cy-os 1 0.250 0.000 1.000 same as
hc-c3-c3-os
c3-c3-cy-cy 1 0.156 0.000 3.000 same as X
-c3-c3-X
c3-c3-cy-os 1 0.156 0.000 3.000 same as X
-c3-c3-X
c3-cy-os-c2 1 0.383 0.000 3.000 same as X
-c3-os-X
cy-cy-os-cy 1 0.383 0.000 3.000 same as
c3-cy-os-cy
c3-c3-cy-h1 1 0.156 0.000 3.000 same as X
-c3-c3-X
cy-cy-os-c2 1 0.383 0.000 3.000 same as
c3-cy-os-c2
cy-os-cy-h1 1 0.383 0.000 3.000 same as X
-c3-os-X
IMPROPER
ca-ca-ca-ha 1.1 180.0 2.0 General
improper torsional angle (2 general atom types)
c3-c3-c2-o 1.1 180.0 2.0 Using default
value
c2-c3-n -hn 1.1 180.0 2.0 General
improper torsional angle (2 general atom types)
c3-o -c2-os 1.1 180.0 2.0 Using default
value
ca-n -c2-o 1.1 180.0 2.0 Using default
value
ca-o -c2-os 1.1 180.0 2.0 Using default
value
NONBON
DU 0.0000 0.0000 ATTN, need revision
---------------------------------------------------------------------------------------------
What do "DU" and "ATTN, need revision" mean in frcmod file?
When I used following commands in tleap,
source leaprc.gaff
LIG = loadmol2 lig.mol2
list
check LIG
I encountered with:
Checking 'LIG'....
Warning: Close contact of 1.417833 angstroms between .R<LIG 1>.A<C19 21>
and .R<LIG 1>.A<H07 69>
Warning: Close contact of 1.134923 angstroms between .R<LIG 1>.A<H06 68>
and .R<LIG 1>.A<H07 69>
Checking parameters for unit 'LIG'.
Checking for bond parameters.
Could not find bond parameter for: DU - c3
Could not find bond parameter for: DU - c3
Could not find bond parameter for: DU - c3
Could not find bond parameter for: DU - ha
Could not find bond parameter for: DU - DU
Could not find bond parameter for: c3 - DU
Checking for angle parameters.
Could not find angle parameter: n - c2 - ca
Could not find angle parameter: n - c2 - o
Could not find angle parameter: c3 - c3 - DU
Could not find angle parameter: c3 - c3 - DU
Could not find angle parameter: DU - c3 - c3
Could not find angle parameter: DU - c3 - c3
Could not find angle parameter: DU - c3 - DU
Could not find angle parameter: DU - c3 - c3
Could not find angle parameter: DU - c3 - c2
Could not find angle parameter: DU - c3 - os
Could not find angle parameter: DU - c3 - h1
Could not find angle parameter: DU - DU - c3
Could not find angle parameter: c3 - DU - c3
Could not find angle parameter: c3 - DU - c3
Could not find angle parameter: c3 - DU - ha
Could not find angle parameter: c3 - DU - DU
Could not find angle parameter: c3 - c3 - DU
Could not find angle parameter: c3 - DU - c3
Could not find angle parameter: c3 - DU - ha
Could not find angle parameter: c3 - DU - DU
Could not find angle parameter: c3 - c3 - DU
Could not find angle parameter: c3 - DU - ha
Could not find angle parameter: c3 - DU - DU
Could not find angle parameter: c2 - os - cy
Could not find angle parameter: ca - c2 - o
Could not find angle parameter: ca - c2 - o
Could not find angle parameter: ca - c2 - os
Could not find angle parameter: o - c2 - os
Could not find angle parameter: o - c2 - os
Could not find angle parameter: o - c2 - os
Could not find angle parameter: o - c2 - os
Could not find angle parameter: ha - DU - DU
There are missing parameters.
check: Warnings: 2
Unit is OK.
How to resolve this issue? Any help will highly be appreciated.
Best,
Shahab
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Received on Fri Sep 16 2016 - 12:30:03 PDT
