Hi,
You probably don’t have all the atoms in your newresidue.lib file that you actually need. That’s what the end of the file is telling you. It’s also telling you that your atom names in DXC don’t match the pdb file.
Systematically go through your lib file and make sure that all your atoms are present exactly as they are in the pdb file. I haven’t used the set model head function before but you have other issues too C5’ and H5’ and H5”.
Maria
> FATAL: Atom .R<DXC 692>.A<P 1> does not have a type.
>
> FATAL: Atom .R<DXC 692>.A<OP1 2> does not have a type.
>
> FATAL: Atom .R<DXC 692>.A<OP2 3> does not have a type.
>
> FATAL: Atom .R<DXC 692>.A<O5' 4> does not have a type.
>
> FATAL: Atom .R<DXC 692>.A<C5' 5> does not have a type.
>
> FATAL: Atom .R<DXC 692>.A<H5' 6> does not have a type.
>
> FATAL: Atom .R<DXC 692>.A<H5'' 7> does not have a type.
> On Oct 8, 2022, at 4:09 PM, Moustafa, Ibrahim M. via AMBER <amber.ambermd.org> wrote:
>
> Dear all,
>
> I am trying to create amber parameters for a non-standard nucleotide.
> I used parameters of standard nucleotide and did the necessary modification.
> I created .frcmod file. In tleap I was able to check the non-standard residue (named DXC) and generate .prmtop & .inpcrd files. I have a problem creating Head & tail atoms before saving .lib file using the commands:
>
> 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.
>
> Also, when I tried to load the full complex in tleap to create .prmtop and .inpcrd files, the new unit is not recognized and FATAL errors appear.
>
> So, when I check the created new residue isolated, I am able to load the .frcmod file and create topology and parameters in tleap. But when I try to do the same for the full complex, it did not work and tleap did not recognize the new residue or the created parameters!
>
> Below is the input for tleap and part of the output.log file.
>
> What am I doing wrong? how to fix it?
>
> Thank you in advance for your help.
>
> Ibrahim
>
>
> source $AMBERHOME/dat/leap/cmd/leaprc.protein.ff14SB
>
> source $AMBERHOME/dat/leap/cmd/leaprc.RNA.OL3
>
> source $AMBERHOME/dat/leap/cmd/leaprc.water.tip3p
>
> logfile ./tleap.log
>
>
> loadamberparams ./newresidue.frcmod
>
> loadoff ./newresidue.lib
>
>
> model = loadpdb "./complex.pdb"
>
>
> check model
>
>
>
>
> /opt/amber/amber22/bin/teLeap: Warning!
>
> Unknown residue: DXC number: 691 type: Terminal/last
>
> ..relaxing end constraints to try for a dbase match
>
>
> /opt/amber/amber22/bin/teLeap: Warning!
>
> -no luck
>
> Creating new UNIT for residue: DXC sequence: 692
>
>
> /opt/amber/amber22/bin/teLeap: Warning!
>
> One sided connection. Residue () missing connect0 atom.
>
> Created a new atom named: P within residue: .R<DXC 692>
>
> Created a new atom named: OP1 within residue: .R<DXC 692>
>
>
> /opt/amber/amber22/bin/teLeap: Warning!
>
> The unperturbed charge of the unit (-37.308100) is not zero.
>
> FATAL: Atom .R<DXC 692>.A<P 1> does not have a type.
>
> FATAL: Atom .R<DXC 692>.A<OP1 2> does not have a type.
>
> FATAL: Atom .R<DXC 692>.A<OP2 3> does not have a type.
>
> FATAL: Atom .R<DXC 692>.A<O5' 4> does not have a type.
>
> FATAL: Atom .R<DXC 692>.A<C5' 5> does not have a type.
>
> FATAL: Atom .R<DXC 692>.A<H5' 6> does not have a type.
>
> FATAL: Atom .R<DXC 692>.A<H5'' 7> does not have a type.
>
>
>
>
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Received on Sat Oct 08 2022 - 14:00:03 PDT
