Well, you have to see if your problematic atoms have corresponding atoms
in the Leap library .. If yes, use a simple shell script and change the
atom names to the one recognized by leap ... if not, you probably have
some issues with your structure that is hard to follow without seeing
and testing the files myself .... However, I cannot help much with that
because I am now traveling and will not be back in the lab until Monday
Vlad
On 03/11/2016 02:26 PM, Sreemol G wrote:
> I have done what you said.. Atoms which were added while loading PDB are
> not defined. Can we delete that atom from the residue from xleap or what
> are the other ways to rectify this error??
>
> On Fri, Mar 11, 2016 at 6:34 PM, Vlad Cojocaru <
> vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>
>> Well, it looks like you have some problems with atom names in the
>> protein as well as some weird bonds in your system ... I am surprized
>> that the protein alone worked well ...
>>
>> Atoms such as HT1, HN ... are not defined in protein residues. You need
>> to sort out what are those atoms in your PDB .. Best is check the
>> residues in xLeap, see what atoms has "ALA" for instance (e.g. type
>> "edit ALA" in xLeap and display atom names) and check whether your PDB
>> contains other atom names. Your PDB will be correctly loaded only if it
>> contains atom names that Leap knows from its residue libraries.
>> Otherwise, Leap fails ...
>>
>> Vlad
>>
>> On 03/11/2016 01:47 PM, Sreemol G wrote:
>>> Actually i have tried but i'm getting errors when i try to save my
>> topology
>>> and coordinate files.I have used the forcefield "leaprc.ff14SB" when i
>>> loaded pdb i got the message and when i tried to save the topology file
>> and
>>> coordinate file i'm getting following error
>>> Created a new atom named: HT1 within residue: .R<NGLY 18>
>>> Created a new atom named: HT2 within residue: .R<NGLY 18>
>>> Created a new atom named: HT3 within residue: .R<NGLY 18>
>>> Created a new atom named: HN within residue: .R<ARG 19>
>>> Created a new atom named: HN within residue: .R<THR 20>
>>> Created a new atom named: HN within residue: .R<ASN 21>
>>> Created a new atom named: HN within residue: .R<LEU 22>
>>> Created a new atom named: HN within residue: .R<ILE 23>
>>> Created a new atom named: HN within residue: .R<VAL 24>
>>> Created a new atom named: HN within residue: .R<ASN 25>
>>> Created a new atom named: HN within residue: .R<TYR 26>
>>> Created a new atom named: HN within residue: .R<LEU 27>
>>> Created a new atom named: HN within residue: .R<GLN 29>
>>> Created a new atom named: HN within residue: .R<ASN 30>
>>> Created a new atom named: HN within residue: .R<MET 31>
>>> Created a new atom named: HN within residue: .R<THR 32>
>>> Created a new atom named: HN within residue: .R<GLN 33>
>>> Created a new atom named: HN within residue: .R<ASP 34>
>>> Created a new atom named: HN within residue: .R<GLU 35>
>>> Created a new atom named: HN within residue: .R<LEU 36>
>>> Created a new atom named: HN within residue: .R<ARG 37>
>>> Created a new atom named: HN within residue: .R<SER 38>
>>> Created a new atom named: HN within residue: .R<LEU 39>
>>> Created a new atom named: HN within residue: .R<PHE 40>
>>> Created a new atom named: HN within residue: .R<SER 41>
>>> Created a new atom named: HN within residue: .R<SER 42>
>>> Created a new atom named: HN within residue: .R<ILE 43>
>>> Created a new atom named: HN within residue: .R<GLY 44>
>>> Created a new atom named: HN within residue: .R<GLU 45>
>>> Created a new atom named: HN within residue: .R<VAL 46>
>>> Created a new atom named: HN within residue: .R<GLU 47>
>>> Created a new atom named: HN within residue: .R<SER 48>
>>> Created a new atom named: HN within residue: .R<ALA 49>
>>> Created a new atom named: HN within residue: .R<LYS 50>
>>> Created a new atom named: HN within residue: .R<LEU 51>
>>> Created a new atom named: HN within residue: .R<ILE 52>
>>> Created a new atom named: HN within residue: .R<ARG 53>
>>> Created a new atom named: HN within residue: .R<ASP 54>
>>> Created a new atom named: HN within residue: .R<LYS 55>
>>> Created a new atom named: HN within residue: .R<VAL 56>
>>> Created a new atom named: HN within residue: .R<ALA 57>
>>> Created a new atom named: HN within residue: .R<GLY 58>
>>> Created a new atom named: HN within residue: .R<HIE 59>
>>> Created a new atom named: HN within residue: .R<SER 60>
>>> Created a new atom named: HN within residue: .R<LEU 61>
>>> Created a new atom named: HN within residue: .R<GLY 62>
>>> Created a new atom named: HN within residue: .R<TYR 63>
>>> Created a new atom named: HN within residue: .R<GLY 64>
>>> Created a new atom named: HN within residue: .R<PHE 65>
>>> Created a new atom named: HN within residue: .R<VAL 66>
>>> Created a new atom named: HN within residue: .R<ASN 67>
>>> Created a new atom named: HN within residue: .R<TYR 68>
>>> Created a new atom named: HN within residue: .R<VAL 69>
>>> Created a new atom named: HN within residue: .R<THR 70>
>>> Created a new atom named: HN within residue: .R<ALA 71>
>>> Created a new atom named: HN within residue: .R<LYS 72>
>>> Created a new atom named: HN within residue: .R<ASP 73>
>>> Created a new atom named: HN within residue: .R<ALA 74>
>>> Created a new atom named: HN within residue: .R<GLU 75>
>>> Created a new atom named: HN within residue: .R<ARG 76>
>>> Created a new atom named: HN within residue: .R<ALA 77>
>>> Created a new atom named: HN within residue: .R<ILE 78>
>>> Created a new atom named: HN within residue: .R<ASN 79>
>>> Created a new atom named: HN within residue: .R<THR 80>
>>> Created a new atom named: HN within residue: .R<LEU 81>
>>> Created a new atom named: HN within residue: .R<ASN 82>
>>> Created a new atom named: HN within residue: .R<GLY 83>
>>> Created a new atom named: HN within residue: .R<LEU 84>
>>> Created a new atom named: HN within residue: .R<ARG 85>
>>> Created a new atom named: HN within residue: .R<LEU 86>
>>> Created a new atom named: HN within residue: .R<GLN 87>
>>> Created a new atom named: HN within residue: .R<SER 88>
>>> Created a new atom named: HN within residue: .R<LYS 89>
>>> Created a new atom named: HN within residue: .R<THR 90>
>>> Created a new atom named: HN within residue: .R<ILE 91>
>>> Created a new atom named: HN within residue: .R<LYS 92>
>>> Created a new atom named: HN within residue: .R<VAL 93>
>>> Created a new atom named: HN within residue: .R<SER 94>
>>> Created a new atom named: HN within residue: .R<TYR 95>
>>> Created a new atom named: HN within residue: .R<ALA 96>
>>> Created a new atom named: HN within residue: .R<ARG 97>
>>> Created a new atom named: HN within residue: .R<SER 99>
>>> Created a new atom named: HN within residue: .R<SER 100>
>>> Created a new atom named: HN within residue: .R<GLU 101>
>>> Created a new atom named: HN within residue: .R<VAL 102>
>>> Created a new atom named: HN within residue: .R<ILE 103>
>>> Created a new atom named: HN within residue: .R<LYS 104>
>>> Created a new atom named: HN within residue: .R<ASP 105>
>>> Created a new atom named: HN within residue: .R<ALA 106>
>>> Created a new atom named: HN within residue: .R<ASN 107>
>>> Created a new atom named: HN within residue: .R<LEU 108>
>>> Created a new atom named: HN within residue: .R<TYR 109>
>>> Created a new atom named: HN within residue: .R<ILE 110>
>>> Created a new atom named: HN within residue: .R<SER 111>
>>> Created a new atom named: HN within residue: .R<GLY 112>
>>> Created a new atom named: HN within residue: .R<LEU 113>
>>> Created a new atom named: HN within residue: .R<ARG 115>
>>> Created a new atom named: HN within residue: .R<THR 116>
>>> Created a new atom named: HN within residue: .R<MET 117>
>>> Created a new atom named: HN within residue: .R<THR 118>
>>> Created a new atom named: HN within residue: .R<GLN 119>
>>> Created a new atom named: HN within residue: .R<LYS 120>
>>> Created a new atom named: HN within residue: .R<ASP 121>
>>> Created a new atom named: HN within residue: .R<VAL 122>
>>> Created a new atom named: HN within residue: .R<GLU 123>
>>> Created a new atom named: HN within residue: .R<ASP 124>
>>> Created a new atom named: HN within residue: .R<MET 125>
>>> Created a new atom named: HN within residue: .R<PHE 126>
>>> Created a new atom named: HN within residue: .R<SER 127>
>>> Created a new atom named: HN within residue: .R<ARG 128>
>>> Created a new atom named: HN within residue: .R<PHE 129>
>>> Created a new atom named: HN within residue: .R<GLY 130>
>>> Created a new atom named: HN within residue: .R<ARG 131>
>>> Created a new atom named: HN within residue: .R<ILE 132>
>>> Created a new atom named: HN within residue: .R<ILE 133>
>>> Created a new atom named: HN within residue: .R<ASN 134>
>>> Created a new atom named: HN within residue: .R<SER 135>
>>> Created a new atom named: HN within residue: .R<ARG 136>
>>> Created a new atom named: HN within residue: .R<VAL 137>
>>> Created a new atom named: HN within residue: .R<LEU 138>
>>> Created a new atom named: HN within residue: .R<VAL 139>
>>> Created a new atom named: HN within residue: .R<ASP 140>
>>> Created a new atom named: HN within residue: .R<GLN 141>
>>> Created a new atom named: HN within residue: .R<THR 142>
>>> Created a new atom named: HN within residue: .R<THR 143>
>>> Created a new atom named: HN within residue: .R<GLY 144>
>>> Created a new atom named: HN within residue: .R<LEU 145>
>>> Created a new atom named: HN within residue: .R<SER 146>
>>> Created a new atom named: HN within residue: .R<ARG 147>
>>> Created a new atom named: HN within residue: .R<GLY 148>
>>> Created a new atom named: HN within residue: .R<VAL 149>
>>> Created a new atom named: HN within residue: .R<ALA 150>
>>> Created a new atom named: HN within residue: .R<PHE 151>
>>> Created a new atom named: HN within residue: .R<ILE 152>
>>> Created a new atom named: HN within residue: .R<ARG 153>
>>> Created a new atom named: HN within residue: .R<PHE 154>
>>> Created a new atom named: HN within residue: .R<ASP 155>
>>> Created a new atom named: HN within residue: .R<LYS 156>
>>> Created a new atom named: HN within residue: .R<ARG 157>
>>> Created a new atom named: HN within residue: .R<SER 158>
>>> Created a new atom named: HN within residue: .R<GLU 159>
>>> Created a new atom named: HN within residue: .R<ALA 160>
>>> Created a new atom named: HN within residue: .R<GLU 161>
>>> Created a new atom named: HN within residue: .R<GLU 162>
>>> Created a new atom named: HN within residue: .R<ALA 163>
>>> Created a new atom named: HN within residue: .R<ILE 164>
>>> Created a new atom named: HN within residue: .R<THR 165>
>>> Created a new atom named: HN within residue: .R<SER 166>
>>> Created a new atom named: HN within residue: .R<PHE 167>
>>> Created a new atom named: HN within residue: .R<ASN 168>
>>> Created a new atom named: HN within residue: .R<GLY 169>
>>> Created a new atom named: HN within residue: .R<HIE 170>
>>> Created a new atom named: HN within residue: .R<LYS 171>
>>> Created a new atom named: OXT within residue: .R<LYS 171>
>>> Created a new atom named: HT1 within residue: .R<GLY 172>
>>> Created a new atom named: HT2 within residue: .R<GLY 172>
>>> Created a new atom named: HT3 within residue: .R<GLY 172>
>>> Created a new atom named: HN within residue: .R<SER 173>
>>> Created a new atom named: HN within residue: .R<SER 174>
>>> Created a new atom named: HN within residue: .R<GLU 175>
>>> Created a new atom named: HN within residue: .R<ILE 177>
>>> Created a new atom named: HN within residue: .R<THR 178>
>>> Created a new atom named: HN within residue: .R<VAL 179>
>>> Created a new atom named: OXT within residue: .R<VAL 179>
>>> Created a new atom named: HT1 within residue: .R<PHE 180>
>>> Created a new atom named: HT2 within residue: .R<PHE 180>
>>> Created a new atom named: HT3 within residue: .R<PHE 180>
>>> Created a new atom named: HN within residue: .R<CALA 181>
>>> total atoms in file: 2291
>>> Leap added 1141 missing atoms according to residue templates:
>>> 1141 H / lone pairs
>>> The file contained 168 atoms not in residue templates
>>>> saveamberparm com com.prmtop com.inpcrd
>>> Checking Unit.
>>> WARNING: There is a bond of 7.785425 angstroms between:
>>> ------- .R<LYS 171>.A<C 21> and .R<GLY 172>.A<N 1>
>>> WARNING: There is a bond of 3.116405 angstroms between:
>>> ------- .R<VAL 179>.A<C 15> and .R<PHE 180>.A<N 1>
>>> WARNING: The unperturbed charge of the unit: -17.000000 is not zero.
>>> FATAL: Atom .R<NGLY 18>.A<HT1 10> does not have a type.
>>> FATAL: Atom .R<NGLY 18>.A<HT2 11> does not have a type.
>>> FATAL: Atom .R<NGLY 18>.A<HT3 12> does not have a type.
>>> FATAL: Atom .R<ARG 19>.A<HN 25> does not have a type.
>>> FATAL: Atom .R<THR 20>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<ASN 21>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<LEU 22>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<ILE 23>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<VAL 24>.A<HN 17> does not have a type.
>>> FATAL: Atom .R<ASN 25>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<TYR 26>.A<HN 22> does not have a type.
>>> FATAL: Atom .R<LEU 27>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<GLN 29>.A<HN 18> does not have a type.
>>> FATAL: Atom .R<ASN 30>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<MET 31>.A<HN 18> does not have a type.
>>> FATAL: Atom .R<THR 32>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<GLN 33>.A<HN 18> does not have a type.
>>> FATAL: Atom .R<ASP 34>.A<HN 13> does not have a type.
>>> FATAL: Atom .R<GLU 35>.A<HN 16> does not have a type.
>>> FATAL: Atom .R<LEU 36>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<ARG 37>.A<HN 25> does not have a type.
>>> FATAL: Atom .R<SER 38>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<LEU 39>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<PHE 40>.A<HN 21> does not have a type.
>>> FATAL: Atom .R<SER 41>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<SER 42>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<ILE 43>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<GLY 44>.A<HN 8> does not have a type.
>>> FATAL: Atom .R<GLU 45>.A<HN 16> does not have a type.
>>> FATAL: Atom .R<VAL 46>.A<HN 17> does not have a type.
>>> FATAL: Atom .R<GLU 47>.A<HN 16> does not have a type.
>>> FATAL: Atom .R<SER 48>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<ALA 49>.A<HN 11> does not have a type.
>>> FATAL: Atom .R<LYS 50>.A<HN 23> does not have a type.
>>> FATAL: Atom .R<LEU 51>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<ILE 52>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<ARG 53>.A<HN 25> does not have a type.
>>> FATAL: Atom .R<ASP 54>.A<HN 13> does not have a type.
>>> FATAL: Atom .R<LYS 55>.A<HN 23> does not have a type.
>>> FATAL: Atom .R<VAL 56>.A<HN 17> does not have a type.
>>> FATAL: Atom .R<ALA 57>.A<HN 11> does not have a type.
>>> FATAL: Atom .R<GLY 58>.A<HN 8> does not have a type.
>>> FATAL: Atom .R<HIE 59>.A<HN 18> does not have a type.
>>> FATAL: Atom .R<SER 60>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<LEU 61>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<GLY 62>.A<HN 8> does not have a type.
>>> FATAL: Atom .R<TYR 63>.A<HN 22> does not have a type.
>>> FATAL: Atom .R<GLY 64>.A<HN 8> does not have a type.
>>> FATAL: Atom .R<PHE 65>.A<HN 21> does not have a type.
>>> FATAL: Atom .R<VAL 66>.A<HN 17> does not have a type.
>>> FATAL: Atom .R<ASN 67>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<TYR 68>.A<HN 22> does not have a type.
>>> FATAL: Atom .R<VAL 69>.A<HN 17> does not have a type.
>>> FATAL: Atom .R<THR 70>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<ALA 71>.A<HN 11> does not have a type.
>>> FATAL: Atom .R<LYS 72>.A<HN 23> does not have a type.
>>> FATAL: Atom .R<ASP 73>.A<HN 13> does not have a type.
>>> FATAL: Atom .R<ALA 74>.A<HN 11> does not have a type.
>>> FATAL: Atom .R<GLU 75>.A<HN 16> does not have a type.
>>> FATAL: Atom .R<ARG 76>.A<HN 25> does not have a type.
>>> FATAL: Atom .R<ALA 77>.A<HN 11> does not have a type.
>>> FATAL: Atom .R<ILE 78>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<ASN 79>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<THR 80>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<LEU 81>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<ASN 82>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<GLY 83>.A<HN 8> does not have a type.
>>> FATAL: Atom .R<LEU 84>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<ARG 85>.A<HN 25> does not have a type.
>>> FATAL: Atom .R<LEU 86>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<GLN 87>.A<HN 18> does not have a type.
>>> FATAL: Atom .R<SER 88>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<LYS 89>.A<HN 23> does not have a type.
>>> FATAL: Atom .R<THR 90>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<ILE 91>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<LYS 92>.A<HN 23> does not have a type.
>>> FATAL: Atom .R<VAL 93>.A<HN 17> does not have a type.
>>> FATAL: Atom .R<SER 94>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<TYR 95>.A<HN 22> does not have a type.
>>> FATAL: Atom .R<ALA 96>.A<HN 11> does not have a type.
>>> FATAL: Atom .R<ARG 97>.A<HN 25> does not have a type.
>>> FATAL: Atom .R<SER 99>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<SER 100>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<GLU 101>.A<HN 16> does not have a type.
>>> FATAL: Atom .R<VAL 102>.A<HN 17> does not have a type.
>>> FATAL: Atom .R<ILE 103>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<LYS 104>.A<HN 23> does not have a type.
>>> FATAL: Atom .R<ASP 105>.A<HN 13> does not have a type.
>>> FATAL: Atom .R<ALA 106>.A<HN 11> does not have a type.
>>> FATAL: Atom .R<ASN 107>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<LEU 108>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<TYR 109>.A<HN 22> does not have a type.
>>> FATAL: Atom .R<ILE 110>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<SER 111>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<GLY 112>.A<HN 8> does not have a type.
>>> FATAL: Atom .R<LEU 113>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<ARG 115>.A<HN 25> does not have a type.
>>> FATAL: Atom .R<THR 116>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<MET 117>.A<HN 18> does not have a type.
>>> FATAL: Atom .R<THR 118>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<GLN 119>.A<HN 18> does not have a type.
>>> FATAL: Atom .R<LYS 120>.A<HN 23> does not have a type.
>>> FATAL: Atom .R<ASP 121>.A<HN 13> does not have a type.
>>> FATAL: Atom .R<VAL 122>.A<HN 17> does not have a type.
>>> FATAL: Atom .R<GLU 123>.A<HN 16> does not have a type.
>>> FATAL: Atom .R<ASP 124>.A<HN 13> does not have a type.
>>> FATAL: Atom .R<MET 125>.A<HN 18> does not have a type.
>>> FATAL: Atom .R<PHE 126>.A<HN 21> does not have a type.
>>> FATAL: Atom .R<SER 127>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<ARG 128>.A<HN 25> does not have a type.
>>> FATAL: Atom .R<PHE 129>.A<HN 21> does not have a type.
>>> FATAL: Atom .R<GLY 130>.A<HN 8> does not have a type.
>>> FATAL: Atom .R<ARG 131>.A<HN 25> does not have a type.
>>> FATAL: Atom .R<ILE 132>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<ILE 133>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<ASN 134>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<SER 135>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<ARG 136>.A<HN 25> does not have a type.
>>> FATAL: Atom .R<VAL 137>.A<HN 17> does not have a type.
>>> FATAL: Atom .R<LEU 138>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<VAL 139>.A<HN 17> does not have a type.
>>> FATAL: Atom .R<ASP 140>.A<HN 13> does not have a type.
>>> FATAL: Atom .R<GLN 141>.A<HN 18> does not have a type.
>>> FATAL: Atom .R<THR 142>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<THR 143>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<GLY 144>.A<HN 8> does not have a type.
>>> FATAL: Atom .R<LEU 145>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<SER 146>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<ARG 147>.A<HN 25> does not have a type.
>>> FATAL: Atom .R<GLY 148>.A<HN 8> does not have a type.
>>> FATAL: Atom .R<VAL 149>.A<HN 17> does not have a type.
>>> FATAL: Atom .R<ALA 150>.A<HN 11> does not have a type.
>>> FATAL: Atom .R<PHE 151>.A<HN 21> does not have a type.
>>> FATAL: Atom .R<ILE 152>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<ARG 153>.A<HN 25> does not have a type.
>>> FATAL: Atom .R<PHE 154>.A<HN 21> does not have a type.
>>> FATAL: Atom .R<ASP 155>.A<HN 13> does not have a type.
>>> FATAL: Atom .R<LYS 156>.A<HN 23> does not have a type.
>>> FATAL: Atom .R<ARG 157>.A<HN 25> does not have a type.
>>> FATAL: Atom .R<SER 158>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<GLU 159>.A<HN 16> does not have a type.
>>> FATAL: Atom .R<ALA 160>.A<HN 11> does not have a type.
>>> FATAL: Atom .R<GLU 161>.A<HN 16> does not have a type.
>>> FATAL: Atom .R<GLU 162>.A<HN 16> does not have a type.
>>> FATAL: Atom .R<ALA 163>.A<HN 11> does not have a type.
>>> FATAL: Atom .R<ILE 164>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<THR 165>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<SER 166>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<PHE 167>.A<HN 21> does not have a type.
>>> FATAL: Atom .R<ASN 168>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<GLY 169>.A<HN 8> does not have a type.
>>> FATAL: Atom .R<HIE 170>.A<HN 18> does not have a type.
>>> FATAL: Atom .R<LYS 171>.A<HN 23> does not have a type.
>>> FATAL: Atom .R<LYS 171>.A<OXT 24> does not have a type.
>>> FATAL: Atom .R<GLY 172>.A<HT1 8> does not have a type.
>>> FATAL: Atom .R<GLY 172>.A<HT2 9> does not have a type.
>>> FATAL: Atom .R<GLY 172>.A<HT3 10> does not have a type.
>>> FATAL: Atom .R<SER 173>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<SER 174>.A<HN 12> does not have a type.
>>> FATAL: Atom .R<GLU 175>.A<HN 16> does not have a type.
>>> FATAL: Atom .R<ILE 177>.A<HN 20> does not have a type.
>>> FATAL: Atom .R<THR 178>.A<HN 15> does not have a type.
>>> FATAL: Atom .R<VAL 179>.A<HN 17> does not have a type.
>>> FATAL: Atom .R<VAL 179>.A<OXT 18> does not have a type.
>>> FATAL: Atom .R<PHE 180>.A<HT1 21> does not have a type.
>>> FATAL: Atom .R<PHE 180>.A<HT2 22> does not have a type.
>>> FATAL: Atom .R<PHE 180>.A<HT3 23> does not have a type.
>>> FATAL: Atom .R<CALA 181>.A<HN 12> does not have a type.
>>> Failed to generate parameters
>>> Parameter file was not saved.
>>>
>>> Can you tell me what may be the reason
>>>
>>> On Fri, Mar 11, 2016 at 6:05 PM, David A Case <david.case.rutgers.edu>
>>> wrote:
>>>
>>>> On Fri, Mar 11, 2016, Sreemol G wrote:
>>>>
>>>>> Can anyone tell me where can i find protein-RNA complex simulation
>>>>> tutorial?? I could able to run simulation for protein and RNA
>> separately
>>>>> with the help of tutorial. But i didnt find tutorial for protein- RNA
>>>>> complex. If anyone knows could you please send it to me??
>>>> Running an RNA-protein complex is no different operationally than for
>> RNA
>>>> or
>>>> protein alone. Don't be afraid to try some experiments, and see what
>> you
>>>> get.
>>>>
>>>> ...dac
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>> --
>> Dr. Vlad Cojocaru
>> Computational Structural Biology Laboratory
>> Department of Cell and Developmental Biology
>> Max Planck Institute for Molecular Biomedicine
>> Röntgenstrasse 20, 48149 Münster, Germany
>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Fri Mar 11 2016 - 06:00:07 PST
