Hi everyone,
When i load a POPC membrane in leap (previously transformed from charmm
through charmmlipid2amber.x) the next message appear:
>> lipid11 = loadamberparams lipid11.dat
Loading parameters: /opt/amber13/dat/leap/parm/lipid11.dat
Reading title:
AMBER Lipid 2011 Force Field (v1.0), A.Skjevik, B. Madej, K.Teigen &
R.C.Walker
>>
>> # Load the Lipid 11 master lib file.
>> loadoff lipid11.lib
Loading library: /opt/amber13/dat/leap/lib/lipid11.lib
Loading: AR
Loading: CHL
Loading: DHA
Loading: LEN
Loading: LEO
Loading: OL
Loading: P2-
Loading: PA
Loading: PC
Loading: PE
Loading: PGR
Loading: PGS
Loading: PH-
Loading: PI
Loading: PS
Loading: ST
>>
>
> mem=loadpdb liptest.pdb
Loading PDB file: ./liptest.pdb
Enter zPdbReadScan from call depth 0.
Warning: name change in pdb file residue 1 ;
this residue is split into PA and PC.
Warning: name change in pdb file residue 1 ;
this residue is split into PC and OL.
2 residues had naming warnings.
There are split residues;
residue sequence numbers will not correspond to those in the pdb.
Exit zPdbReadScan from call depth 0.
Matching PDB residue names to LEaP variables.
(Residue 0: PA, Terminal/beginning, was not found in name map.)
(Residue 1: PC, Nonterminal, was not found in name map.)
(Residue 2: OL, Terminal/last, was not found in name map.)
Joining PA - PC
Joining PC - OL
total atoms in file: 134
> check mem
Checking 'mem'....
Checking parameters for unit 'mem'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
Searching in the mail list archive i didnīt find much info about that.
Checking the molecule seems to be right.
Are these warnings normal? May I skip them? Or there is something missed?
Thank you so much.
Carlos T. Nieto
_________________________________________________
Carlos T. Nieto
Organic Chemistry Department
University of Salamanca
Avda de los Caidos s/n
37008 Salamanca
SPAIN
T: 00 34 923294474
Fax: 00 34 923294574
email:eneas.usal.es
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Received on Thu Jun 27 2013 - 08:30:03 PDT
