Dear Amber Users,
I have just started using Amber, in order to use the GLYCAM06 force field. The aim is to get the topology files and convert them to GROMACS format later, by which our simulations are being performed.
In order to do so, I am using tleap to extract the topology files. I have modelled a crystalline cellulose in Materials Studio and exported the pdf format. I have then used the pdb4amber to convert it to amber format (attached ambertest.pdb file). Apparently, the file seems to have multiple duplicated atoms leading to the following warnings.
Could you please help me what the problem is arising from and how to solve it?
mol = loadpdb ambertest.pdb
Loading PDB file: ./ambertest.pdb
-- residue 1: duplicate [ C11] atoms (total 170)
-- residue 1: duplicate [ C12] atoms (total 180)
-- residue 1: duplicate [ C21] atoms (total 170)
-- residue 1: duplicate [ C22] atoms (total 180)
-- residue 1: duplicate [ C31] atoms (total 170)
-- residue 1: duplicate [ C32] atoms (total 180)
-- residue 1: duplicate [ C41] atoms (total 170)
-- residue 1: duplicate [ C42] atoms (total 180)
-- residue 1: duplicate [ C51] atoms (total 170)
-- residue 1: duplicate [ C52] atoms (total 180)
-- residue 1: duplicate [ C61] atoms (total 170)
-- residue 1: duplicate [ C62] atoms (total 180)
-- residue 1: duplicate [ H11] atoms (total 170)
-- residue 1: duplicate [ H12] atoms (total 180)
-- residue 1: duplicate [ H21] atoms (total 170)
-- residue 1: duplicate [ H22] atoms (total 180)
-- residue 1: duplicate [ H31] atoms (total 170)
-- residue 1: duplicate [ H32] atoms (total 180)
-- residue 1: duplicate [ H41] atoms (total 170)
-- residue 1: duplicate [ H42] atoms (total 180)
-- residue 1: duplicate [ H51] atoms (total 170)
-- residue 1: duplicate [ H52] atoms (total 180)
-- residue 1: duplicate [ O11] atoms (total 170)
-- residue 1: duplicate [ O12] atoms (total 180)
-- residue 1: duplicate [ O21] atoms (total 170)
-- residue 1: duplicate [ O22] atoms (total 180)
-- residue 1: duplicate [ O31] atoms (total 170)
-- residue 1: duplicate [ O32] atoms (total 180)
-- residue 1: duplicate [ O51] atoms (total 170)
-- residue 1: duplicate [ O52] atoms (total 180)
-- residue 1: duplicate [ O61] atoms (total 170)
-- residue 1: duplicate [ O62] atoms (total 180)
-- residue 1: duplicate [AH61] atoms (total 170)
-- residue 1: duplicate [AH62] atoms (total 180)
-- residue 1: duplicate [BH61] atoms (total 170)
-- residue 1: duplicate [BH62] atoms (total 180)
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.)
Warning: Unknown residue: MOL number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
Warning: -no luck
Creating new UNIT for residue: MOL sequence: 1
Created a new atom named: C12 within residue: .R<MOL 1>
Created a new atom named: H12 within residue: .R<MOL 1>
Created a new atom named: C22 within residue: .R<MOL 1>
Created a new atom named: H22 within residue: .R<MOL 1>
Created a new atom named: C32 within residue: .R<MOL 1>
Created a new atom named: H32 within residue: .R<MOL 1>
Created a new atom named: C42 within residue: .R<MOL 1>
Created a new atom named: H42 within residue: .R<MOL 1>
Created a new atom named: C52 within residue: .R<MOL 1>
Created a new atom named: H52 within residue: .R<MOL 1>
Created a new atom named: C62 within residue: .R<MOL 1>
Created a new atom named: AH62 within residue: .R<MOL 1>
Created a new atom named: BH62 within residue: .R<MOL 1>
Created a new atom named: O22 within residue: .R<MOL 1>
Created a new atom named: O32 within residue: .R<MOL 1>
Created a new atom named: O12 within residue: .R<MOL 1>
Created a new atom named: O52 within residue: .R<MOL 1>
Created a new atom named: O62 within residue: .R<MOL 1>
Created a new atom named: C11 within residue: .R<MOL 1>
Created a new atom named: H11 within residue: .R<MOL 1>
Created a new atom named: C21 within residue: .R<MOL 1>
Created a new atom named: H21 within residue: .R<MOL 1>
Created a new atom named: C31 within residue: .R<MOL 1>
Created a new atom named: H31 within residue: .R<MOL 1>
Created a new atom named: C41 within residue: .R<MOL 1>
Created a new atom named: H41 within residue: .R<MOL 1>
Created a new atom named: C51 within residue: .R<MOL 1>
Created a new atom named: H51 within residue: .R<MOL 1>
Created a new atom named: C61 within residue: .R<MOL 1>
Created a new atom named: AH61 within residue: .R<MOL 1>
Created a new atom named: BH61 within residue: .R<MOL 1>
Created a new atom named: O21 within residue: .R<MOL 1>
Created a new atom named: O31 within residue: .R<MOL 1>
Created a new atom named: O11 within residue: .R<MOL 1>
Created a new atom named: O51 within residue: .R<MOL 1>
Created a new atom named: O61 within residue: .R<MOL 1>
total atoms in file: 6300
The file contained 36 atoms not in residue templates
> saveamberparm mol ambertest.prmtop ambertest.inpcrd
Checking Unit.
FATAL: Atom .R<MOL 1>.A<C12 1> does not have a type.
FATAL: Atom .R<MOL 1>.A<H12 2> does not have a type.
FATAL: Atom .R<MOL 1>.A<C22 3> does not have a type.
FATAL: Atom .R<MOL 1>.A<H22 4> does not have a type.
FATAL: Atom .R<MOL 1>.A<C32 5> does not have a type.
FATAL: Atom .R<MOL 1>.A<H32 6> does not have a type.
FATAL: Atom .R<MOL 1>.A<C42 7> does not have a type.
FATAL: Atom .R<MOL 1>.A<H42 8> does not have a type.
FATAL: Atom .R<MOL 1>.A<C52 9> does not have a type.
FATAL: Atom .R<MOL 1>.A<H52 10> does not have a type.
FATAL: Atom .R<MOL 1>.A<C62 11> does not have a type.
FATAL: Atom .R<MOL 1>.A<AH62 12> does not have a type.
FATAL: Atom .R<MOL 1>.A<BH62 13> does not have a type.
FATAL: Atom .R<MOL 1>.A<O22 14> does not have a type.
FATAL: Atom .R<MOL 1>.A<O32 15> does not have a type.
FATAL: Atom .R<MOL 1>.A<O12 16> does not have a type.
FATAL: Atom .R<MOL 1>.A<O52 17> does not have a type.
FATAL: Atom .R<MOL 1>.A<O62 18> does not have a type.
FATAL: Atom .R<MOL 1>.A<C11 19> does not have a type.
FATAL: Atom .R<MOL 1>.A<H11 20> does not have a type.
FATAL: Atom .R<MOL 1>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 1>.A<H21 22> does not have a type.
FATAL: Atom .R<MOL 1>.A<C31 23> does not have a type.
FATAL: Atom .R<MOL 1>.A<H31 24> does not have a type.
FATAL: Atom .R<MOL 1>.A<C41 25> does not have a type.
FATAL: Atom .R<MOL 1>.A<H41 26> does not have a type.
FATAL: Atom .R<MOL 1>.A<C51 27> does not have a type.
FATAL: Atom .R<MOL 1>.A<H51 28> does not have a type.
FATAL: Atom .R<MOL 1>.A<C61 29> does not have a type.
FATAL: Atom .R<MOL 1>.A<AH61 30> does not have a type.
FATAL: Atom .R<MOL 1>.A<BH61 31> does not have a type.
FATAL: Atom .R<MOL 1>.A<O21 32> does not have a type.
FATAL: Atom .R<MOL 1>.A<O31 33> does not have a type.
FATAL: Atom .R<MOL 1>.A<O11 34> does not have a type.
FATAL: Atom .R<MOL 1>.A<O51 35> does not have a type.
FATAL: Atom .R<MOL 1>.A<O61 36> does not have a type.
Error: Failed to generate parameters
Warning: Parameter file was not saved.
Thank you in advance.
Regards,
Ali
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Received on Wed Oct 17 2018 - 11:30:02 PDT
