Thank you Maria and David.
I checked the pdb and atom names matches the lib file exactly.
Yes, I checked the unit using commands "desc model & desc model.DXC" before saving the .lib file.
That is how I created the new unit:
1. Used xparmed to write .fomcrd of a standard nucleotide
2. (2`-deoxy-CMP) from .prmtop file of previous simulation
3. modified the .fomcrd file to match the new unit (3`-deoxy-CMP).
4. Created a .mol2 file for the 3`-deoxy-CMP
5. In xleap I checked the parameters and saved .lib file
6. In tleap I loaded the newresidue.fomcrd & newresidue.lib and checked the unit, I was able to create a .prmtop & .inpcrd of the new unit (isolated)
Here is the .lib file:
!!index array str
"model1"
!entry.model1.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"P" "P" 0 1 131072 1 15 1.165900
"OP1" "O2" 0 1 131072 2 8 -0.776100
"OP2" "O2" 0 1 131072 3 8 -0.776100
"O5'" "OS" 0 1 131072 4 8 -0.495400
"C5'" "CJ" 0 1 131072 5 6 -0.006900
"H5'" "H1" 0 1 131072 6 1 0.075400
"H5''" "H1" 0 1 131072 7 1 0.075400
"C4'" "CT" 0 1 131072 8 6 0.162900
"H4'" "H1" 0 1 131072 9 1 0.117600
"O4'" "OS" 0 1 131072 10 8 -0.369100
"C1'" "CT" 0 1 131072 11 6 -0.011600
"H1'" "H2" 0 1 131072 12 1 0.196300
"N1" "N*" 0 1 131072 13 7 -0.033900
"C6" "C1" 0 1 131072 14 6 -0.018300
"H6" "H4" 0 1 131072 15 1 0.229300
"C5" "C1" 0 1 131072 16 6 -0.522200
"H5" "HA" 0 1 131072 17 1 0.186300
"C4" "CA" 0 1 131072 18 6 0.843900
"N4" "N2" 0 1 131072 19 7 -0.977300
"H41" "H" 0 1 131072 20 1 0.431400
"H42" "H" 0 1 131072 21 1 0.431400
"N3" "NC" 0 1 131072 22 7 -0.774800
"C2" "C" 0 1 131072 23 6 0.795900
"O2" "O" 0 1 131072 24 8 -0.654800
"C3'" "CT" 0 1 131072 25 6 -0.085400
"H3'" "HC" 0 1 131072 26 1 0.071800
"C2'" "C7" 0 1 131072 27 6 0.071300
"H2'" "H1" 0 1 131072 28 1 0.098500
"O2'" "OH" 0 1 131072 29 8 -0.654900
"HO2'" "HO" 0 1 131072 30 1 0.439600
"H3''" "HC" 0 1 131072 31 1 0.071800
!entry.model1.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
"P" "P" 0 -1 0.0
"OP1" "O2" 0 -1 0.0
"OP2" "O2" 0 -1 0.0
"O5'" "OS" 0 -1 0.0
"C5'" "CJ" 0 -1 0.0
"H5'" "H1" 0 -1 0.0
"H5''" "H1" 0 -1 0.0
"C4'" "CT" 0 -1 0.0
"H4'" "H1" 0 -1 0.0
"O4'" "OS" 0 -1 0.0
"C1'" "CT" 0 -1 0.0
"H1'" "H2" 0 -1 0.0
"N1" "N*" 0 -1 0.0
"C6" "C1" 0 -1 0.0
"H6" "H4" 0 -1 0.0
"C5" "C1" 0 -1 0.0
"H5" "HA" 0 -1 0.0
"C4" "CA" 0 -1 0.0
"N4" "N2" 0 -1 0.0
"H41" "H" 0 -1 0.0
"H42" "H" 0 -1 0.0
"N3" "NC" 0 -1 0.0
"C2" "C" 0 -1 0.0
"O2" "O" 0 -1 0.0
"C3'" "CT" 0 -1 0.0
"H3'" "HC" 0 -1 0.0
"C2'" "C7" 0 -1 0.0
"H2'" "H1" 0 -1 0.0
"O2'" "OH" 0 -1 0.0
"HO2'" "HO" 0 -1 0.0
"H3''" "HC" 0 -1 0.0
!entry.model1.unit.boundbox array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.model1.unit.childsequence single int
2
!entry.model1.unit.connect array int
1
29
!entry.model1.unit.connectivity table int atom1x int atom2x int flags
1 2 1
1 3 2
1 4 1
4 5 1
5 6 1
5 7 1
5 8 1
8 9 1
8 10 1
8 25 1
10 11 1
11 12 1
11 13 1
11 27 1
13 14 1
13 23 1
14 15 1
14 16 2
16 17 1
16 18 1
18 19 1
18 22 2
19 20 1
19 21 1
22 23 1
23 24 2
25 26 1
25 27 1
25 31 1
27 28 1
27 29 1
29 30 1
!entry.model1.unit.hierarchy table str abovetype int abovex str belowtype int belowx
"U" 0 "R" 1
"R" 1 "A" 1
"R" 1 "A" 2
"R" 1 "A" 3
"R" 1 "A" 4
"R" 1 "A" 5
"R" 1 "A" 6
"R" 1 "A" 7
"R" 1 "A" 8
"R" 1 "A" 9
"R" 1 "A" 10
"R" 1 "A" 11
"R" 1 "A" 12
"R" 1 "A" 13
"R" 1 "A" 14
"R" 1 "A" 15
"R" 1 "A" 16
"R" 1 "A" 17
"R" 1 "A" 18
"R" 1 "A" 19
"R" 1 "A" 20
"R" 1 "A" 21
"R" 1 "A" 22
"R" 1 "A" 23
"R" 1 "A" 24
"R" 1 "A" 25
"R" 1 "A" 26
"R" 1 "A" 27
"R" 1 "A" 28
"R" 1 "A" 29
"R" 1 "A" 30
"R" 1 "A" 31
!entry.model1.unit.name single str
"DXC"
!entry.model1.unit.positions table dbl x dbl y dbl z
37.466000 69.867000 92.016000
37.668000 68.518000 92.570000
36.788000 69.947000 90.717000
36.701000 70.751000 93.058000
35.532000 70.315000 93.729000
34.873000 69.771000 93.052000
35.012000 71.203000 94.081000
35.871000 69.450000 94.938000
36.328000 68.519000 94.604000
36.773000 70.130000 95.796000
36.466000 69.844000 97.152000
37.354000 69.475000 97.673000
35.961000 71.072000 97.840000
35.749000 72.258000 97.173000
35.947000 72.326000 96.108000
35.301000 73.347000 97.848000
35.135000 74.275000 97.322000
35.103000 73.213000 99.250000
34.697000 74.225000 99.965000
34.642000 74.091000 100.958000
34.511000 75.110000 99.527000
35.327000 72.100000 99.911000
35.767000 71.019000 99.226000
35.975000 69.985000 99.854000
34.667000 69.109000 95.808000
34.057000 69.998000 95.967000
35.398000 68.742000 97.100000
34.725000 68.767000 97.958000
36.057000 67.482000 97.012000
36.541000 67.287000 97.838000
34.089000 68.276000 95.408000
!entry.model1.unit.residueconnect table int c1x int c2x int c3x int c4x int c5x int c6x
0 0 0 0 0 0
!entry.model1.unit.residues table str name int seq int childseq int startatomx str restype int imagingx
"DXC" 1 32 1 "?" 0
!entry.model1.unit.residuesPdbSequenceNumber array int
0
!entry.model1.unit.solventcap array dbl
-1.000000
0.0
0.0
0.0
0.0
!entry.model1.unit.velocities table dbl x dbl y dbl z
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
0.0 0.0 0.0
Also, in tleap after the warning and FATAL errors from the complex.pdb, when I check the unit using "desc model.DXC" I get the correct information (but missing the connect information):
> desc model.DXC
RESIDUE name: DXC
RESIDUE sequence number: 692
RESIDUE PDB sequence number: 692
Type: undefined
Connection atoms:
Improper torsions:
Contents:
A<P 1>
A<OP1 2>
A<OP2 3>
A<O5' 4>
A<C5' 5>
A<H5' 6>
A<H5'' 7>
A<C4' 8>
A<H4' 9>
A<O4' 10>
A<C1' 11>
A<H1' 12>
A<N1 13>
A<C6 14>
A<H6 15>
A<C5 16>
A<H5 17>
A<C4 18>
A<N4 19>
A<H41 20>
A<H42 21>
A<N3 22>
A<C2 23>
A<O2 24>
A<C3' 25>
A<H3' 26>
A<C2' 27>
A<H2' 28>
A<O2' 29>
A<HO2' 30>
A<H3'' 31>
Thanks,
Ibrahim
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Saturday, October 8, 2022 9:35 PM
To: Moustafa, Ibrahim M. <ria2.psu.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] parameterization for non-standard nucleotide
On Sat, Oct 08, 2022, Moustafa, Ibrahim M. via AMBER wrote:
>
>set model head model.DXC.P
>saveoff model newresidue.lib
>
>The commands work. But when I tried to check the created library in tleap
>again I don't see the Head information in the saved .lib file.
Before or after the saveoff command, you could use the desc command in tleap
to see what is in the unit; eg. "desc model.DXC". (Is this what you meant
when you say "check the created library in tleap"?)
>loadoff ./newresidue.lib
>model = loadpdb "./complex.pdb"
As Maria noted, it is likely that the residue or atom names in complex.pdb
don't match those in newresidue.lib. In tleap, use the "list" command to
see what units are loaded, and "desc" command to see the properties of the
units that you have. Using a text editor is generally the easiest way to
examine the pdb file.
...hope this helps. If not, you may have to explain how you made the new
unit, probably posting the newresidue.lib file.
....dac
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Received on Sat Oct 08 2022 - 21:30:02 PDT
