Hi,
Have a closer look at your protein structure
*WARNING: There is a bond of 30.093865 angstroms between: *
*------- .R<SER 859>.A<C 10> and .R<SER 860>.A<N 1>*
There is a bond distortion which will lead to serious errors layer on.
*FATAL: Atom .R<LIG 1253>.A<C 35> does not have a type.*
*FATAL: Atom .R<LIG 1253>.A<N 36> does not have a type.*
*FATAL: Atom .R<LIG 1253>.A<S 37> does not have a type.*
*FATAL: Atom .R<LIG 1253>.A<O 38> does not have a type.*
*FATAL: Atom .R<LIG 1253>.A<H 39> does not have a type.*
*FATAL: Atom .R<LIG 1253>.A<Cl 40> does not have a type.*
For this, check if the atom names are identical in the lib files you loaded.
Best Regards
Elvis A F Martis
Molecular Simulations Group,
Department of Pharmaceutical Chemistry,
Bombay College of Pharmacy,
Kalina, Santacruz [E],
Mumbai 400098,
INDIA.
Institute Web-address: www.bcp.edu.in<http://www.bcp.edu.in>
Research Group Web-address: www.profeccoutinho.net.in<http://www.profeccoutinho.net.in>
Personal Web-address: www.elvismartis.in
________________________________
From: Mac Kevin Braza <mebraza.up.edu.ph>
Sent: 26 December 2018 10:06
To: AMBER.ambermd.org
Subject: [AMBER] FATAL Error: Atom does not have a type
Hello all,
I am preparing 2 ligands in complex with a GPCR in tLEaP after
parameterizing each component separately (i.e. antechamber, parmchk, and
tleap). However, whenever I combined them with cat command and read them as
complex this error occured which I do not understand. I attached here the
my input file and the log file (truncated) leap when I submitted it.
>From leap.log file:
*1 residue had naming warnings.*
* There are split residues;*
* residue sequence numbers will not correspond to those in the pdb.*
*-- residue 1253: duplicate [ C] atoms (total 15)*
*-- residue 1253: duplicate [ N] atoms (total 3)*
*-- residue 1253: duplicate [ O] atoms (total 2)*
*-- residue 1253: duplicate [Cl] atoms (total 2)*
* 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.)*
*Created a new atom named: C within residue: .R<LIG 1253>*
*Created a new atom named: N within residue: .R<LIG 1253>*
*Created a new atom named: S within residue: .R<LIG 1253>*
*Created a new atom named: O within residue: .R<LIG 1253>*
*Created a new atom named: H within residue: .R<LIG 1253>*
*Created a new atom named: Cl within residue: .R<LIG 1253>*
* total atoms in file: 227566*
* The file contained 6 atoms not in residue templates*
*Checking Unit.*
*WARNING: There is a bond of 30.093865 angstroms between: *
*------- .R<SER 859>.A<C 10> and .R<SER 860>.A<N 1>*
*FATAL: Atom .R<LIG 1253>.A<C 35> does not have a type.*
*FATAL: Atom .R<LIG 1253>.A<N 36> does not have a type.*
*FATAL: Atom .R<LIG 1253>.A<S 37> does not have a type.*
*FATAL: Atom .R<LIG 1253>.A<O 38> does not have a type.*
*FATAL: Atom .R<LIG 1253>.A<H 39> does not have a type.*
*FATAL: Atom .R<LIG 1253>.A<Cl 40> does not have a type.*
*Failed to generate parameters*
*Parameter file was not saved.*
* Quit*
Thank you in advance!
Best regards,
Mac Kevin E. Braza
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Received on Tue Dec 25 2018 - 21:00:05 PST
