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 - 07:00:03 PDT
