Thank you Anselm and prof. Case so much. I edited the .lib file and changed "model" to "DXC" and it worked. Also, saveMol3 trick worked (just a note, it required options 0 or 1 for the command to run):
>saveMol3 DXC file.mol2 1
0: for default atom types
1: for amber atom types
The resulting mol2 file has "head" and "tail" information.
Thank you for your help
Ibrahim
________________________________
From: Dr. Anselm Horn via AMBER <amber.ambermd.org>
Sent: Monday, October 10, 2022 7:54 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] parameterization for non-standard nucleotide
Ibrahim,
from your file I guess instead of "model1" there should occur the name
of your new residue i.e. "DXC": tleap already complained that the
residue DXC is unknown (from your previous e-mail):
Unknown residue: DXC number: 691 type: Terminal/last
Try to substitute all occurrences of model1 by DXC in your lib file and
rerun tleap.
Maybe you want to try out a minimal test case first (e.g. via the
sequence command in tleap) to check that your parameters work within the
Amber framework at all. If you succeed, go on to your real case, and
also check for special cases (terminal vs. mid-sequence residue etc.).
Best regards,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 09.10.2022 um 06:18 schrieb Moustafa, Ibrahim M. via AMBER:
> 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 Tue Oct 11 2022 - 07:00:04 PDT
