Dear Sebastian,
The residue (unit) name in file.lib is "mol" while in the PDB is "H1A"... you need to rename it so it is called the same in both files, e.g.:
from shell do:
sed 's/mol/H1A/' file.lib > file2.lib
In leap console execute:
source oldff/leaprc.ff99SB
loadoff file2.lib
mol = loadpdb file2.pdb
#------------------------
The issue you had is probably because you created the unit by loading the PDB of the single residue into the variable name "mol" and then just saved the lib file, so the unit took the var name... that happens because a unit may be a residue or a something more complex (e.g. a water box)... so if you want a unit to have a particular name in a lib then the var name must be chosen accordingly...
Best,
MatÃas
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/laboratorios-eng/lsbm]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Sebastian Muraru" <sebastian.muraru.grabtop.upb.ro>
Para: amber.ambermd.org
Enviados: Martes, 10 de Julio 2018 10:46:33
Asunto: [AMBER] Xleap does not (?) loadoff lib files
Dear All,
This is the first time I am sending a message to the mailing list, I hope I am doing it the right way.
I have a question regarding importing a lib file into xleap. I have created a lib file using xleap, which from my understanding should describe a new residue. However, when loading a pdb file containing that specific residue, the atoms/residue do not get recognized - basically it is as if nothing gets imported. I am using AmberTools18 installed through conda.
If I wrongly understood the way things are supposed to work, I apologise in advance.
The commands I go through after launching xleap are basically:
source oldff/leaprc.ff99SB
loadoff file.lib
mol = loadpdb file2.pdb
- this is when I notice the residues do not get recognized.
The pdb file I was trying to use the lib file for, looks like this:
_ _ _ _ _ _
###START###
ATOM 1 OL H1A 1 7.37 0.0 1.49 1.00 0.00
ATOM 2 HK H1A 1 6.448 -0.097 1.809 1.00 0.00
###END###
_ _ _ _ _ _
And the lib file I have created looks like this:
_ _ _ _ _
###START####
!!index array str
"mol"
!entry.mol.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"OL" "OH" 0 1 131075 1 8 -0.651400
"HK" "HO" 0 1 131075 2 1 0.447400
!entry.mol.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
"OL" "OH" 0 -1 0.0
"HK" "HO" 0 -1 0.0
!entry.mol.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.mol.unit.childsequence single int
2
!entry.mol.unit.connect array int
0
0
!entry.mol.unit.connectivity table int atom1x int atom2x int flags
1 2 17
!entry.mol.unit.hierarchy table str abovetype int abovex str belowtype int belowx
"U" 0 "R" 1
"R" 1 "A" 1
"R" 1 "A" 2
!entry.mol.unit.name single str
"H1A"
!entry.mol.unit.positions table dbl x dbl y dbl z
7.557000 1.219000 2.190000
7.557000 1.219000 3.170000
!entry.mol.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
0 0 0 0 0 0
!entry.mol.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
"H1A" 1 3 1 "?" 0
!entry.mol.unit.residuesPdbSequenceNumber array int
1
!entry.mol.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.mol.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 0.0 0.0
###END###
_ _ _ _ _
I appreciate the time you took to read this,
Best,
Sebastian
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Received on Tue Jul 10 2018 - 08:30:02 PDT
