If anybody can suggest any reason for the error as in the mail I wrote.
Is this a problem with the Amber version?
Thank you,
Maya
---------- Forwarded message ---------
From: maya nair <mayasnair1.gmail.com>
Date: Tue, Oct 3, 2023 at 6:00 PM
Subject: Re: [Sender Not Verified] [AMBER] Query regarding two ligands with
one DNA
To: Steinbrecher, Thomas <thomas.steinbrecher.roche.com>
Thank you Dr.Thomas.
I corrected the atom names as per the .lib and the pdb file made without
any errors.
I tried to run a simple minimization. I tried with energy minimization for
DNA starting structures using the input below with and without distance
restraints as below.
&cntrl
imin=1, maxcyc=1000, ncyc=1000, maxcyc=1000, ncyc=1000, ntpr=20,
ntb=0, cut=10.0, nmropt = 1,
/
&ewald
eedmeth=5,
/
LISTOUT=POUT
DISTANG=RST
Without distance, it is giving the error,
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
#0 0x7F25D916FE08
#1 0x7F25D916EF90
#2 0x7F25D88A04BF
#3 0x56EC57 in __nblist_MOD_grid_ucell
#4 0x5725D2 in __nblist_MOD_nonbond_list
#5 0x720E0C in force_
#6 0x4E7C8D in runmin_
#7 0x4D3B5B in sander_
#8 0x4CB40D in MAIN__ at multisander.F90:?
[1]+ Segmentation fault (core dumped) sander -O -i min.in -o
complex_min.out -p newcomplexamber3.prmtop -c newcomplexamber3.rst7 -r
complex_min.ncrst
With distance,
[2] 14252
[1] Exit 1 sander -O -i min.in -o complex_min.out -p
newcomplexamber3.prmtop -c newcomplexamber3.rst7 -r complex_min.ncrst.
Can you please suggest any correction needed in the file.
I want to put the ligands in their places using the distance file which
include distances in DNA and DNA to ligands.
Thank you for your attention.
Maya
On Tue, Oct 3, 2023 at 4:37 PM Steinbrecher, Thomas <
thomas.steinbrecher.roche.com> wrote:
> Hi Maya,
>
> how do you define your ligand residues? The error you post indicates that
> the residue definition in Amber (from a .lib file for example) does not
> match the atom names in your input PDB. There is nothing special about two
> ligands binding (non-covalently I assume?) to DNA, I suspect the issue is
> not related to that. Is it possible that your PDB has only the element
> symbol as atom name for the ligands? Check the parameter files for your
> ligand residues and make sure the atom names in there match the PDB ligand
> atoms. It may help to build Amber files for each component of your system
> separately to isolate errors, then build the whole system once all issues
> are fixed.
>
> Kind Regards,
>
> Thomas
>
> On Tue, Oct 3, 2023 at 12:55 PM maya nair via AMBER <amber.ambermd.org>
> wrote:
>
>> **Warning** The sender address (maya nair via AMBER ) can not be
>> verified, sender email address could be spoofed. Please take care to
>> proceed.
>> Dear Prof. David,
>> Can you please suggest how to make a pdb structure for DNA with two
>> ligands. Our NMR data showed two ligand molecules binding to a quadruplex
>> DNA. But I am facing problem in making the pdb structure. When I add two
>> datasets for the same ligand, it says
>>
>> Loading PDB file: ./newcomplexamber3.pdb
>> -- residue 25: duplicate [ C] atoms (total 14)
>> -- residue 25: duplicate [ H] atoms (total 12)
>> -- residue 25: duplicate [ O] atoms (total 3)
>> -- residue 26: duplicate [ C] atoms (total 14)
>> -- residue 26: duplicate [ H] atoms (total 12)
>> -- residue 26: duplicate [ O] atoms (total 3)
>>
>> Warning: Atom names in each residue should be unique.
>> (Same-name atoms are handled by using the first
>> occurrence and by ignoring the rest.
>> Frequently duplicate atom names stem from alternate
>> conformations in the PDB file.)
>>
>> Added missing heavy atom: .R<UNK 25>.A<C2 6>
>> Added missing heavy atom: .R<UNK 25>.A<C3 7>
>> Added missing heavy atom: .R<UNK 25>.A<C1 5>
>> Added missing heavy atom: .R<UNK 25>.A<C8 12>
>> Added missing heavy atom: .R<UNK 25>.A<C9 13>
>> Added missing heavy atom: .R<UNK 25>.A<C11 15>
>> Added missing heavy atom: .R<UNK 25>.A<C12 16>
>> Added missing heavy atom: .R<UNK 25>.A<C13 17>
>> Added missing heavy atom: .R<UNK 25>.A<O2 3>
>> Added missing heavy atom: .R<UNK 25>.A<C4 8>
>> Added missing heavy atom: .R<UNK 25>.A<C5 9>
>> Added missing heavy atom: .R<UNK 25>.A<C7 11>
>> Added missing heavy atom: .R<UNK 25>.A<C6 10>
>> Added missing heavy atom: .R<UNK 25>.A<O1 2>
>> Added missing heavy atom: .R<UNK 25>.A<C10 14>
>> Added missing heavy atom: .R<UNK 26>.A<C2 6>
>> Added missing heavy atom: .R<UNK 26>.A<C3 7>
>> Added missing heavy atom: .R<UNK 26>.A<C1 5>
>> Added missing heavy atom: .R<UNK 26>.A<C8 12>
>> Added missing heavy atom: .R<UNK 26>.A<C9 13>
>> Added missing heavy atom: .R<UNK 26>.A<C11 15>
>> Added missing heavy atom: .R<UNK 26>.A<C12 16>
>> Added missing heavy atom: .R<UNK 26>.A<C13 17>
>> Added missing heavy atom: .R<UNK 26>.A<O2 3>
>> Added missing heavy atom: .R<UNK 26>.A<C4 8>
>> Added missing heavy atom: .R<UNK 26>.A<C5 9>
>> Added missing heavy atom: .R<UNK 26>.A<C7 11>
>> Added missing heavy atom: .R<UNK 26>.A<C6 10>
>> Added missing heavy atom: .R<UNK 26>.A<O1 2>
>> Added missing heavy atom: .R<UNK 26>.A<C10 14>
>> total atoms in file: 778
>> Leap added 52 missing atoms according to residue templates:
>> 30 Heavy
>> 22 H / lone pair
>> Residue 25 and 26 are the ligands. I changed the names of the ligands and
>> tried. Its not working.How I change the atom names?
>> Please suggest.
>> Thanks
>> Maya
>> --
>> Maya S Nair
>> Assistant Professor
>> Department of Biotechnology
>> IIT Roorkee
>> India
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
> --
> *Dr. Thomas Steinbrecher*
> Principal Scientist CADD
>
> Roche Pharma Research and Early Development
> Roche Innovation Center Basel
> F. Hoffmann-La Roche Ltd
> Bldg. 092/3.92
> Grenzacherstrasse 124
> 4070 Basel
> Switzerland
>
> Phone +41 61 682 1319
> mailto: thomas.steinbrecher.roche.com
>
--
Maya S Nair
Assistant Professor
Department of Biotechnology
IIT Roorkee
India
--
Maya S Nair
Assistant Professor
Department of Biotechnology
IIT Roorkee
India
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Received on Wed Oct 04 2023 - 11:30:02 PDT
