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From: Bill Ross <ross.cgl.ucsf.edu>

Date: Thu, 21 Jan 2016 18:41:59 -0800

It looks like your atom names for the given atoms in the pdb are not

present in the residue template, either because they are extra, or far

more likely because they are mis-named or the names are mis-formatted.

E.g. in leap

* > desc NASN
*

and see what the pdb's H and HB1 atoms are the template, and fix the pdb

atom names.

And so on. Maybe you'll find an atom alignment problem, or something

similar where a few editing commands can fix the file.

Bill

On 1/21/16 5:00 PM, Luis Esteban wrote:

*> Dear User Amber
*

*>
*

*> I have a problem when I used tleap, the problem is the next:
*

*>
*

*> Leap added 4 missing atoms according to residue templates:
*

*> 1 Heavy
*

*> 3 H / lone pairs
*

*> The file contained 401 atoms not in residue templates
*

*>
*

*> When I try to save the file I have this problem:
*

*>
*

*>> saveamberparm prr prr.prmtop prr.inpcrd
*

*> Checking Unit.
*

*> FATAL: Atom .R<NASN 1>.A<H 17> does not have a type.
*

*> FATAL: Atom .R<NASN 1>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<GLU 2>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 2>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<PHE 3>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<SER 4>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<ILE 5>.A<HG11 20> does not have a type.
*

*> FATAL: Atom .R<ILE 5>.A<HD1 21> does not have a type.
*

*> FATAL: Atom .R<ILE 5>.A<HD2 22> does not have a type.
*

*> FATAL: Atom .R<ILE 5>.A<HD3 23> does not have a type.
*

*> FATAL: Atom .R<LEU 6>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<LYS 7>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<LYS 7>.A<HG1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 7>.A<HD1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 7>.A<HE1 26> does not have a type.
*

*> FATAL: Atom .R<SER 8>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<PRO 9>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 9>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 9>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<GLY 10>.A<HA1 8> does not have a type.
*

*> FATAL: Atom .R<SER 11>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<PHE 14>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<ARG 15>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<ARG 15>.A<HG1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 15>.A<HD1 27> does not have a type.
*

*> FATAL: Atom .R<ASN 16>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<GLY 17>.A<HA1 8> does not have a type.
*

*> FATAL: Atom .R<ASN 18>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<TRP 19>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<PRO 20>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 20>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 20>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<ILE 21>.A<HG11 20> does not have a type.
*

*> FATAL: Atom .R<ILE 21>.A<HD1 21> does not have a type.
*

*> FATAL: Atom .R<ILE 21>.A<HD2 22> does not have a type.
*

*> FATAL: Atom .R<ILE 21>.A<HD3 23> does not have a type.
*

*> FATAL: Atom .R<PRO 22>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 22>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 22>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<GLY 23>.A<HA1 8> does not have a type.
*

*> FATAL: Atom .R<GLU 24>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 24>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<ARG 25>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<ARG 25>.A<HG1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 25>.A<HD1 27> does not have a type.
*

*> FATAL: Atom .R<ILE 26>.A<HG11 20> does not have a type.
*

*> FATAL: Atom .R<ILE 26>.A<HD1 21> does not have a type.
*

*> FATAL: Atom .R<ILE 26>.A<HD2 22> does not have a type.
*

*> FATAL: Atom .R<ILE 26>.A<HD3 23> does not have a type.
*

*> FATAL: Atom .R<PRO 27>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 27>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 27>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<ASP 28>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<LEU 32>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<SER 33>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<MET 34>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<MET 34>.A<HG1 19> does not have a type.
*

*> FATAL: Atom .R<GLY 35>.A<HA1 8> does not have a type.
*

*> FATAL: Atom .R<PHE 36>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<SER 37>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<LYS 39>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<LYS 39>.A<HG1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 39>.A<HD1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 39>.A<HE1 26> does not have a type.
*

*> FATAL: Atom .R<GLU 40>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 40>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<ASP 41>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<LEU 42>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<SER 43>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<TRP 44>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<PRO 45>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 45>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 45>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<GLY 46>.A<HA1 8> does not have a type.
*

*> FATAL: Atom .R<LEU 47>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<GLY 50>.A<HA1 8> does not have a type.
*

*> FATAL: Atom .R<ASN 51>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<LEU 52>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<PHE 53>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<HIE 54>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<ARG 55>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<ARG 55>.A<HG1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 55>.A<HD1 27> does not have a type.
*

*> FATAL: Atom .R<PRO 56>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 56>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 56>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<ARG 57>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<ARG 57>.A<HG1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 57>.A<HD1 27> does not have a type.
*

*> FATAL: Atom .R<MET 61>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<MET 61>.A<HG1 19> does not have a type.
*

*> FATAL: Atom .R<MET 63>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<MET 63>.A<HG1 19> does not have a type.
*

*> FATAL: Atom .R<LYS 65>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<LYS 65>.A<HG1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 65>.A<HD1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 65>.A<HE1 26> does not have a type.
*

*> FATAL: Atom .R<GLY 66>.A<HA1 8> does not have a type.
*

*> FATAL: Atom .R<ASN 68>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<LYS 69>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<LYS 69>.A<HG1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 69>.A<HD1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 69>.A<HE1 26> does not have a type.
*

*> FATAL: Atom .R<LEU 70>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<LEU 72>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<PRO 73>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 73>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 73>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<PRO 74>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 74>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 74>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<GLY 75>.A<HA1 8> does not have a type.
*

*> FATAL: Atom .R<SER 76>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<ILE 78>.A<HG11 20> does not have a type.
*

*> FATAL: Atom .R<ILE 78>.A<HD1 21> does not have a type.
*

*> FATAL: Atom .R<ILE 78>.A<HD2 22> does not have a type.
*

*> FATAL: Atom .R<ILE 78>.A<HD3 23> does not have a type.
*

*> FATAL: Atom .R<SER 79>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<TYR 80>.A<HB1 22> does not have a type.
*

*> FATAL: Atom .R<PRO 81>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 81>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 81>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<LEU 82>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<GLU 83>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 83>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<ASN 84>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 87>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 87>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 87>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<PHE 88>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<SER 89>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<LEU 90>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<ASP 91>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 92>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<ASN 95>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<SER 96>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<ILE 97>.A<HG11 20> does not have a type.
*

*> FATAL: Atom .R<ILE 97>.A<HD1 21> does not have a type.
*

*> FATAL: Atom .R<ILE 97>.A<HD2 22> does not have a type.
*

*> FATAL: Atom .R<ILE 97>.A<HD3 23> does not have a type.
*

*> FATAL: Atom .R<HID 98>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<SER 99>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<LEU 100>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<PHE 101>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<SER 102>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<GLU 103>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 103>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<GLU 104>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 104>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<PRO 106>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 106>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 106>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<LEU 109>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<GLN 110>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<GLN 110>.A<HG1 19> does not have a type.
*

*> FATAL: Atom .R<LEU 111>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<PRO 113>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 113>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 113>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<SER 114>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<GLU 115>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 115>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<GLU 116>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 116>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<ARG 117>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<ARG 117>.A<HG1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 117>.A<HD1 27> does not have a type.
*

*> FATAL: Atom .R<TYR 119>.A<HB1 22> does not have a type.
*

*> FATAL: Atom .R<MET 120>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<MET 120>.A<HG1 19> does not have a type.
*

*> FATAL: Atom .R<GLY 122>.A<HA1 8> does not have a type.
*

*> FATAL: Atom .R<LYS 123>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<LYS 123>.A<HG1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 123>.A<HD1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 123>.A<HE1 26> does not have a type.
*

*> FATAL: Atom .R<ASN 125>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<SER 126>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<PHE 128>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<GLU 129>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 129>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<ASP 130>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<LEU 131>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<SER 132>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<LEU 135>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<ARG 136>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<ARG 136>.A<HG1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 136>.A<HD1 27> does not have a type.
*

*> FATAL: Atom .R<GLN 137>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<GLN 137>.A<HG1 19> does not have a type.
*

*> FATAL: Atom .R<LEU 138>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<ARG 139>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<ARG 139>.A<HG1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 139>.A<HD1 27> does not have a type.
*

*> FATAL: Atom .R<ASN 140>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<ARG 141>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<ARG 141>.A<HG1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 141>.A<HD1 27> does not have a type.
*

*> FATAL: Atom .R<LEU 142>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<PHE 143>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<GLN 144>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<GLN 144>.A<HG1 19> does not have a type.
*

*> FATAL: Atom .R<GLU 145>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 145>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<ASN 146>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<SER 147>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<LEU 149>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<SER 150>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<SER 151>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<LEU 152>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<PRO 153>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 153>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 153>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<LEU 154>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<ASN 155>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<SER 156>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<LEU 157>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<SER 158>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<ARG 159>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<ARG 159>.A<HG1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 159>.A<HD1 27> does not have a type.
*

*> FATAL: Atom .R<ASN 160>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<ASN 161>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<GLU 162>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 162>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<ASP 164>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<LEU 165>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<LEU 166>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<PHE 167>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<LEU 168>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<SER 169>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<GLU 170>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 170>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<LEU 171>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<GLN 172>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<GLN 172>.A<HG1 19> does not have a type.
*

*> FATAL: Atom .R<LEU 174>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<HIE 175>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<ASP 176>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<ILE 177>.A<HG11 20> does not have a type.
*

*> FATAL: Atom .R<ILE 177>.A<HD1 21> does not have a type.
*

*> FATAL: Atom .R<ILE 177>.A<HD2 22> does not have a type.
*

*> FATAL: Atom .R<ILE 177>.A<HD3 23> does not have a type.
*

*> FATAL: Atom .R<SER 178>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<SER 179>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<LEU 180>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<LEU 181>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<SER 182>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<ARG 183>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<ARG 183>.A<HG1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 183>.A<HD1 27> does not have a type.
*

*> FATAL: Atom .R<HID 184>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<LYS 185>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<LYS 185>.A<HG1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 185>.A<HD1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 185>.A<HE1 26> does not have a type.
*

*> FATAL: Atom .R<HIE 186>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<LEU 187>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<LYS 189>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<LYS 189>.A<HG1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 189>.A<HD1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 189>.A<HE1 26> does not have a type.
*

*> FATAL: Atom .R<ASP 190>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<HIE 191>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<SER 192>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<PRO 193>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 193>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 193>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<ASP 194>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<LEU 195>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<TYR 196>.A<HB1 22> does not have a type.
*

*> FATAL: Atom .R<SER 197>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<LEU 198>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<GLU 199>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 199>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<LEU 200>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<GLY 202>.A<HA1 8> does not have a type.
*

*> FATAL: Atom .R<LEU 203>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<ASP 204>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<GLU 205>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 205>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<ILE 206>.A<HG11 20> does not have a type.
*

*> FATAL: Atom .R<ILE 206>.A<HD1 21> does not have a type.
*

*> FATAL: Atom .R<ILE 206>.A<HD2 22> does not have a type.
*

*> FATAL: Atom .R<ILE 206>.A<HD3 23> does not have a type.
*

*> FATAL: Atom .R<GLY 207>.A<HA1 8> does not have a type.
*

*> FATAL: Atom .R<LYS 208>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<LYS 208>.A<HG1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 208>.A<HD1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 208>.A<HE1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 209>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<ARG 209>.A<HG1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 209>.A<HD1 27> does not have a type.
*

*> FATAL: Atom .R<TYR 210>.A<HB1 22> does not have a type.
*

*> FATAL: Atom .R<GLY 211>.A<HA1 8> does not have a type.
*

*> FATAL: Atom .R<GLU 212>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 212>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<ASP 213>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 214>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<GLU 215>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 215>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<GLN 216>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<GLN 216>.A<HG1 19> does not have a type.
*

*> FATAL: Atom .R<PHE 217>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<ARG 218>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<ARG 218>.A<HG1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 218>.A<HD1 27> does not have a type.
*

*> FATAL: Atom .R<ASP 219>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 221>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<LYS 222>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<LYS 222>.A<HG1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 222>.A<HD1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 222>.A<HE1 26> does not have a type.
*

*> FATAL: Atom .R<ILE 223>.A<HG11 20> does not have a type.
*

*> FATAL: Atom .R<ILE 223>.A<HD1 21> does not have a type.
*

*> FATAL: Atom .R<ILE 223>.A<HD2 22> does not have a type.
*

*> FATAL: Atom .R<ILE 223>.A<HD3 23> does not have a type.
*

*> FATAL: Atom .R<LEU 224>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<ASP 226>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<LEU 228>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<GLN 229>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<GLN 229>.A<HG1 19> does not have a type.
*

*> FATAL: Atom .R<LYS 230>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<LYS 230>.A<HG1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 230>.A<HD1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 230>.A<HE1 26> does not have a type.
*

*> FATAL: Atom .R<PHE 231>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<ASP 233>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<ASP 234>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<MET 235>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<MET 235>.A<HG1 19> does not have a type.
*

*> FATAL: Atom .R<TYR 236>.A<HB1 22> does not have a type.
*

*> FATAL: Atom .R<SER 237>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<LEU 238>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<TYR 239>.A<HB1 22> does not have a type.
*

*> FATAL: Atom .R<GLY 240>.A<HA1 8> does not have a type.
*

*> FATAL: Atom .R<GLY 241>.A<HA1 8> does not have a type.
*

*> FATAL: Atom .R<ASN 242>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<GLU 246>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 246>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<LEU 247>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<LYS 251>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<LYS 251>.A<HG1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 251>.A<HD1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 251>.A<HE1 26> does not have a type.
*

*> FATAL: Atom .R<SER 252>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<PHE 253>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<ASP 254>.A<HB1 13> does not have a type.
*

*> FATAL: Atom .R<SER 256>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<LEU 257>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<ILE 258>.A<HG11 20> does not have a type.
*

*> FATAL: Atom .R<ILE 258>.A<HD1 21> does not have a type.
*

*> FATAL: Atom .R<ILE 258>.A<HD2 22> does not have a type.
*

*> FATAL: Atom .R<ILE 258>.A<HD3 23> does not have a type.
*

*> FATAL: Atom .R<ARG 259>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<ARG 259>.A<HG1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 259>.A<HD1 27> does not have a type.
*

*> FATAL: Atom .R<LYS 260>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<LYS 260>.A<HG1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 260>.A<HD1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 260>.A<HE1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 262>.A<HB1 25> does not have a type.
*

*> FATAL: Atom .R<ARG 262>.A<HG1 26> does not have a type.
*

*> FATAL: Atom .R<ARG 262>.A<HD1 27> does not have a type.
*

*> FATAL: Atom .R<ILE 264>.A<HG11 20> does not have a type.
*

*> FATAL: Atom .R<ILE 264>.A<HD1 21> does not have a type.
*

*> FATAL: Atom .R<ILE 264>.A<HD2 22> does not have a type.
*

*> FATAL: Atom .R<ILE 264>.A<HD3 23> does not have a type.
*

*> FATAL: Atom .R<LEU 265>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<GLU 266>.A<HB1 16> does not have a type.
*

*> FATAL: Atom .R<GLU 266>.A<HG1 17> does not have a type.
*

*> FATAL: Atom .R<LYS 268>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<LYS 268>.A<HG1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 268>.A<HD1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 268>.A<HE1 26> does not have a type.
*

*> FATAL: Atom .R<GLN 269>.A<HB1 18> does not have a type.
*

*> FATAL: Atom .R<GLN 269>.A<HG1 19> does not have a type.
*

*> FATAL: Atom .R<LYS 271>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<LYS 271>.A<HG1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 271>.A<HD1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 271>.A<HE1 26> does not have a type.
*

*> FATAL: Atom .R<ASN 272>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 273>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 273>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 273>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<SER 275>.A<HB1 12> does not have a type.
*

*> FATAL: Atom .R<PRO 276>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PRO 276>.A<HG1 16> does not have a type.
*

*> FATAL: Atom .R<PRO 276>.A<HD1 17> does not have a type.
*

*> FATAL: Atom .R<TYR 277>.A<HB1 22> does not have a type.
*

*> FATAL: Atom .R<ASN 278>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<LEU 279>.A<HB1 20> does not have a type.
*

*> FATAL: Atom .R<TYR 281>.A<HB1 22> does not have a type.
*

*> FATAL: Atom .R<LYS 282>.A<HB1 23> does not have a type.
*

*> FATAL: Atom .R<LYS 282>.A<HG1 24> does not have a type.
*

*> FATAL: Atom .R<LYS 282>.A<HD1 25> does not have a type.
*

*> FATAL: Atom .R<LYS 282>.A<HE1 26> does not have a type.
*

*> FATAL: Atom .R<TYR 283>.A<HB1 22> does not have a type.
*

*> FATAL: Atom .R<ASN 284>.A<HB1 15> does not have a type.
*

*> FATAL: Atom .R<PHE 285>.A<HB1 21> does not have a type.
*

*> FATAL: Atom .R<CGLU 286>.A<HB1 17> does not have a type.
*

*> FATAL: Atom .R<CGLU 286>.A<HG1 18> does not have a type.
*

*> Failed to generate parameters
*

*> Parameter file was not saved.
*

*>
*

*> Could you help me.....
*

*>
*

*> Beast regards
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

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Received on Thu Jan 21 2016 - 19:00:03 PST

Date: Thu, 21 Jan 2016 18:41:59 -0800

It looks like your atom names for the given atoms in the pdb are not

present in the residue template, either because they are extra, or far

more likely because they are mis-named or the names are mis-formatted.

E.g. in leap

and see what the pdb's H and HB1 atoms are the template, and fix the pdb

atom names.

And so on. Maybe you'll find an atom alignment problem, or something

similar where a few editing commands can fix the file.

Bill

On 1/21/16 5:00 PM, Luis Esteban wrote:

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Received on Thu Jan 21 2016 - 19:00:03 PST

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