There is a PDB standard that limits the number of columns for each
field. People attempt to work around the limitation in incompatible ways.
On 1/9/21 3:44 PM, Eduardo R. Almeida wrote:
> Dear Bill Ross,
>
> Is there a limit for the number of residues? I'm asking this since I have more then 9999 residues of water molecules. This way, the residues are duplicated through my pdb file.
>
>
>
>
>
>
> ________________________________
> De: Bill Ross <ross.cgl.ucsf.edu>
> Enviado: sábado, 9 de janeiro de 2021 20:31
> Para: amber.ambermd.org <amber.ambermd.org>
> Assunto: Re: [AMBER] Error in xleap: water molecules
>
> Residue numberings must be unique to the residue.
>
> Bill
>
> On 1/9/21 3:29 PM, Eduardo R. Almeida wrote:
>> Dears David A. Case and Bill Ross,
>>
>> Thank you for your help.
>>
>> I'll try to remove waters from the end of the file in order to localize the problem. However, when you asked me the first error, what I previously showed was actually the first error after loading the pdb file in xleap. After loading the pdb file, I got some warnings related to the split of the lipid residues:
>>
>> ****************************************************
>>> com_mem = loadpdb com_mem.pdb
>> Loading PDB file: ./com_mem.pdb
>>
>> Warning: Name change in pdb file residue 1 ;
>> this residue is split into OL and PE.
>>
>> Warning: Name change in pdb file residue 1 ;
>> this residue is split into PE and OL.
>>
>> Warning: Name change in pdb file residue 2 ;
>> this residue is split into OL and PE.
>>
>> Warning: Name change in pdb file residue 2 ;
>> this residue is split into PE and OL.
>>
>> Warning: Name change in pdb file residue 3 ;
>> this residue is split into OL and PS.
>>
>> *****************************************************
>>
>> These warnings continue for all lipid molecules in the lipid bilayer (my system). After that, the warnings referring to the water molecules were presented:
>>
>> ******************************************************
>>
>> Warning: Name change in pdb file residue 326 ;
>> this residue is split into PC and OL.
>>
>> Note: 512 residues had naming warnings.
>> Thus, there are split residues;
>> residue sequence numbers will not correspond to those in the pdb.
>> -- residue 19812: duplicate [ H1] atoms (total 10)
>> -- residue 19812: duplicate [ H2] atoms (total 10)
>> -- residue 19812: duplicate [ O] atoms (total 10)
>> -- residue 19813: duplicate [ H1] atoms (total 10)
>> -- residue 19813: duplicate [ H2] atoms (total 10)
>> -- residue 19813: duplicate [ O] atoms (total 10)
>> -- residue 19814: duplicate [ H1] atoms (total 10)
>> -- residue 19814: duplicate [ H2] atoms (total 10)
>> -- residue 19814: duplicate [ O] atoms (total 10)
>> -- residue 19815: duplicate [ H1] atoms (total 10)
>> -- residue 19815: duplicate [ H2] atoms (total 10)
>> -- residue 19815: duplicate [ O] atoms (total 10)
>> -- residue 19816: duplicate [ H1] atoms (total 10)
>> -- residue 19816: duplicate [ H2] atoms (total 10)
>> -- residue 19816: duplicate [ O] atoms (total 10)
>> -- residue 19817: duplicate [ H1] atoms (total 10)
>> -- residue 19817: duplicate [ H2] atoms (total 10)
>> -- residue 19817: duplicate [ O] atoms (total 10)
>> -- residue 19818: duplicate [ H1] atoms (total 10)
>> -- residue 19818: duplicate [ H2] atoms (total 10)
>> -- residue 19818: duplicate [ O] atoms (total 10)
>> -- residue 19819: duplicate [ H1] atoms (total 10)
>> -- residue 19819: duplicate [ H2] atoms (total 10)
>> -- residue 19819: duplicate [ O] atoms (total 10)
>> -- residue 19820: duplicate [ H1] atoms (total 10)
>> -- residue 19820: duplicate [ H2] atoms (total 10)
>> -- residue 19820: duplicate [ O] atoms (total 10)
>> -- residue 19821: duplicate [ H1] atoms (total 10)
>> -- residue 19821: duplicate [ H2] atoms (total 10)
>> -- residue 19821: duplicate [ O] atoms (total 10)
>> -- residue 19822: duplicate [ H1] atoms (total 10)
>> -- residue 19822: duplicate [ H2] atoms (total 10)
>> -- residue 19822: duplicate [ O] atoms (total 10)
>> -- residue 19823: duplicate [ H1] atoms (total 10)
>> -- residue 19823: duplicate [ H2] atoms (total 10)
>> -- residue 19823: duplicate [ O] atoms (total 10)
>> -- residue 19824: duplicate [ H1] atoms (total 10)
>> -- residue 19824: duplicate [ H2] atoms (total 10)
>> -- residue 19824: duplicate [ O] atoms (total 10)
>> -- residue 19825: duplicate [ H1] atoms (total 10)
>> -- residue 19825: duplicate [ H2] atoms (total 10)
>> -- residue 19825: duplicate [ O] atoms (total 10)
>> -- residue 19826: duplicate [ H1] atoms (total 10)
>> -- residue 19826: duplicate [ H2] atoms (total 10)
>> -- residue 19826: duplicate [ O] atoms (total 10)
>> -- residue 19827: duplicate [ H1] atoms (total 10)
>> -- residue 19827: duplicate [ H2] atoms (total 10)
>> -- residue 19827: duplicate [ O] atoms (total 10)
>> -- residue 19828: duplicate [ H1] atoms (total 10)
>> -- residue 19828: duplicate [ H2] atoms (total 10)
>> -- residue 19828: duplicate [ O] atoms (total 10)
>> -- residue 19829: duplicate [ H1] atoms (total 10)
>> -- residue 19829: duplicate [ H2] atoms (total 10)
>> -- residue 19829: duplicate [ O] atoms (total 10)
>> -- residue 19830: duplicate [ H1] atoms (total 10)
>> -- residue 19830: duplicate [ H2] atoms (total 10)
>> -- residue 19830: duplicate [ O] atoms (total 10)
>> -- residue 19831: duplicate [ H1] atoms (total 10)
>> -- residue 19831: duplicate [ H2] atoms (total 10)
>> -- residue 19831: duplicate [ O] atoms (total 10)
>> -- residue 19832: duplicate [ H1] atoms (total 10)
>> -- residue 19832: duplicate [ H2] atoms (total 10)
>> -- residue 19832: duplicate [ O] atoms (total 10)
>> -- residue 19833: duplicate [ H1] atoms (total 10)
>> -- residue 19833: duplicate [ H2] atoms (total 10)
>> -- residue 19833: duplicate [ O] atoms (total 10)
>> -- residue 19834: duplicate [ H1] atoms (total 10)
>> -- residue 19834: duplicate [ H2] atoms (total 10)
>> -- residue 19834: duplicate [ O] atoms (total 10)
>> -- residue 19835: duplicate [ H1] atoms (total 10)
>> -- residue 19835: duplicate [ H2] atoms (total 10)
>> -- residue 19835: duplicate [ O] atoms (total 10)
>> -- residue 19836: duplicate [ H1] atoms (total 10)
>> -- residue 19836: duplicate [ H2] atoms (total 10)
>> -- residue 19836: duplicate [ O] atoms (total 10)
>> -- residue 19837: duplicate [ H1] atoms (total 10)
>> -- residue 19837: duplicate [ H2] atoms (total 10)
>> -- residue 19837: duplicate [ O] atoms (total 10)
>> -- residue 19838: duplicate [ H1] atoms (total 10)
>> -- residue 19838: duplicate [ H2] atoms (total 10)
>> -- residue 19838: duplicate [ O] atoms (total 10)
>> -- residue 19839: duplicate [ H1] atoms (total 10)
>> -- residue 19839: duplicate [ H2] atoms (total 10)
>> -- residue 19839: duplicate [ O] atoms (total 10)
>> -- residue 19840: duplicate [ H1] atoms (total 10)
>> -- residue 19840: duplicate [ H2] atoms (total 10)
>> -- residue 19840: duplicate [ O] atoms (total 10)
>> -- residue 19841: duplicate [ H1] atoms (total 10)
>> -- residue 19841: duplicate [ H2] atoms (total 10)
>> -- residue 19841: duplicate [ O] atoms (total 10)
>> -- residue 19842: duplicate [ H1] atoms (total 10)
>> -- residue 19842: duplicate [ H2] atoms (total 10)
>> -- residue 19842: duplicate [ O] atoms (total 10)
>> -- residue 19843: duplicate [ H1] atoms (total 10)
>> -- residue 19843: duplicate [ H2] atoms (total 10)
>> -- residue 19843: duplicate [ O] atoms (total 10)
>> -- residue 19844: duplicate [ H1] atoms (total 10)
>> -- residue 19844: duplicate [ H2] atoms (total 10)
>> -- residue 19844: duplicate [ O] atoms (total 10)
>> -- residue 19845: duplicate [ H1] atoms (total 10)
>> -- residue 19845: duplicate [ H2] atoms (total 10)
>> -- residue 19845: duplicate [ O] atoms (total 10)
>> -- residue 19846: duplicate [ H1] atoms (total 10)
>> -- residue 19846: duplicate [ H2] atoms (total 10)
>> -- residue 19846: duplicate [ O] atoms (total 10)
>> -- residue 19847: duplicate [ H1] atoms (total 10)
>> -- residue 19847: duplicate [ H2] atoms (total 10)
>> -- residue 19847: duplicate [ O] atoms (total 10)
>> -- residue 19848: duplicate [ H1] atoms (total 10)
>> -- residue 19848: duplicate [ H2] atoms (total 10)
>> -- residue 19848: duplicate [ O] atoms (total 10)
>> -- residue 19849: duplicate [ H1] atoms (total 10)
>> -- residue 19849: duplicate [ H2] atoms (total 10)
>> -- residue 19849: duplicate [ O] atoms (total 10)
>> -- residue 19850: duplicate [ H1] atoms (total 10)
>> -- residue 19850: duplicate [ H2] atoms (total 10)
>> -- residue 19850: duplicate [ O] atoms (total 10)
>> -- residue 19851: duplicate [ H1] atoms (total 10)
>> -- residue 19851: duplicate [ H2] atoms (total 10)
>> -- residue 19851: duplicate [ O] atoms (total 10)
>> -- residue 19852: duplicate [ H1] atoms (total 10)
>> -- residue 19852: duplicate [ H2] atoms (total 10)
>> -- residue 19852: duplicate [ O] atoms (total 10)
>> -- residue 19853: duplicate [ H1] atoms (total 10)
>> -- residue 19853: duplicate [ H2] atoms (total 10)
>> -- residue 19853: duplicate [ O] atoms (total 10)
>> -- residue 19854: duplicate [ H1] atoms (total 10)
>> -- residue 19854: duplicate [ H2] atoms (total 10)
>> -- residue 19854: duplicate [ O] atoms (total 10)
>> -- residue 19855: duplicate [ H1] atoms (total 10)
>> -- residue 19855: duplicate [ H2] atoms (total 10)
>> -- residue 19855: duplicate [ O] atoms (total 10)
>> -- residue 19856: duplicate [ H1] atoms (total 10)
>> -- residue 19856: duplicate [ H2] atoms (total 10)
>> -- residue 19856: duplicate [ O] atoms (total 10)
>> -- residue 19857: duplicate [ H1] atoms (total 10)
>> -- residue 19857: duplicate [ H2] atoms (total 10)
>> -- residue 19857: duplicate [ O] atoms (total 10)
>> -- residue 19858: duplicate [ H1] atoms (total 10)
>> -- residue 19858: duplicate [ H2] atoms (total 10)
>> -- residue 19858: duplicate [ O] atoms (total 10)
>> -- residue 19859: duplicate [ H1] atoms (total 10)
>> -- residue 19859: duplicate [ H2] atoms (total 10)
>> -- residue 19859: duplicate [ O] atoms (total 10)
>> -- residue 19860: duplicate [ H1] atoms (total 10)
>> -- residue 19860: duplicate [ H2] atoms (total 10)
>> -- residue 19860: duplicate [ O] atoms (total 10)
>> -- residue 19861: duplicate [ H1] atoms (total 10)
>> -- residue 19861: duplicate [ H2] atoms (total 10)
>> -- residue 19861: duplicate [ O] atoms (total 10)
>> -- residue 19862: duplicate [ H1] atoms (total 10)
>> -- residue 19862: duplicate [ H2] atoms (total 10)
>> -- residue 19862: duplicate [ O] atoms (total 10)
>> -- residue 19863: duplicate [ H1] atoms (total 10)
>> -- residue 19863: duplicate [ H2] atoms (total 10)
>> -- residue 19863: duplicate [ O] atoms (total 10)
>> -- residue 19864: duplicate [ H1] atoms (total 10)
>> -- residue 19864: duplicate [ H2] atoms (total 10)
>> -- residue 19864: duplicate [ O] atoms (total 10)
>> -- residue 19865: duplicate [ H1] atoms (total 10)
>> -- residue 19865: duplicate [ H2] atoms (total 10)
>> -- residue 19865: duplicate [ O] atoms (total 10)
>> -- residue 19866: duplicate [ H1] atoms (total 10)
>> -- residue 19866: duplicate [ H2] atoms (total 10)
>> -- residue 19866: duplicate [ O] atoms (total 10)
>> -- residue 19867: duplicate [ H1] atoms (total 10)
>> -- residue 19867: duplicate [ H2] atoms (total 10)
>> -- residue 19867: duplicate [ O] atoms (total 10)
>> -- residue 19868: duplicate [ H1] atoms (total 10)
>> -- residue 19868: duplicate [ H2] atoms (total 10)
>> -- residue 19868: duplicate [ O] atoms (total 10)
>> -- residue 19869: duplicate [ H1] atoms (total 10)
>> -- residue 19869: duplicate [ H2] atoms (total 10)
>> -- residue 19869: duplicate [ O] atoms (total 10)
>> -- residue 19870: duplicate [ H1] atoms (total 10)
>> -- residue 19870: duplicate [ H2] atoms (total 10)
>> -- residue 19870: duplicate [ O] atoms (total 10)
>> -- residue 19871: duplicate [ H1] atoms (total 10)
>> -- residue 19871: duplicate [ H2] atoms (total 10)
>> -- residue 19871: duplicate [ O] atoms (total 10)
>> -- residue 19872: duplicate [ H1] atoms (total 10)
>> -- residue 19872: duplicate [ H2] atoms (total 10)
>> -- residue 19872: duplicate [ O] atoms (total 10)
>> -- residue 19873: duplicate [ H1] atoms (total 10)
>> -- residue 19873: duplicate [ H2] atoms (total 10)
>> -- residue 19873: duplicate [ O] atoms (total 10)
>> -- residue 19874: duplicate [ H1] atoms (total 10)
>> -- residue 19874: duplicate [ H2] atoms (total 10)
>> -- residue 19874: duplicate [ O] atoms (total 10)
>> -- residue 19875: duplicate [ H1] atoms (total 10)
>> -- residue 19875: duplicate [ H2] atoms (total 10)
>> -- residue 19875: duplicate [ O] atoms (total 10)
>> -- residue 19876: duplicate [ H1] atoms (total 10)
>> -- residue 19876: duplicate [ H2] atoms (total 10)
>> -- residue 19876: duplicate [ O] atoms (total 10)
>> -- residue 19877: duplicate [ H1] atoms (total 10)
>> -- residue 19877: duplicate [ H2] atoms (total 10)
>> -- residue 19877: duplicate [ O] atoms (total 10)
>> -- residue 19878: duplicate [ H1] atoms (total 10)
>> -- residue 19878: duplicate [ H2] atoms (total 10)
>> -- residue 19878: duplicate [ O] atoms (total 10)
>> -- residue 19879: duplicate [ H1] atoms (total 10)
>> -- residue 19879: duplicate [ H2] atoms (total 10)
>> -- residue 19879: duplicate [ O] atoms (total 10)
>> -- residue 19880: duplicate [ H1] atoms (total 10)
>> -- residue 19880: duplicate [ H2] atoms (total 10)
>> -- residue 19880: duplicate [ O] atoms (total 10)
>> -- residue 19881: duplicate [ H1] atoms (total 10)
>> -- residue 19881: duplicate [ H2] atoms (total 10)
>> -- residue 19881: duplicate [ O] atoms (total 10)
>> -- residue 19882: duplicate [ H1] atoms (total 10)
>> -- residue 19882: duplicate [ H2] atoms (total 10)
>> -- residue 19882: duplicate [ O] atoms (total 10)
>> -- residue 19883: duplicate [ H1] atoms (total 10)
>> -- residue 19883: duplicate [ H2] atoms (total 10)
>> -- residue 19883: duplicate [ O] atoms (total 10)
>> -- residue 19884: duplicate [ H1] atoms (total 10)
>> -- residue 19884: duplicate [ H2] atoms (total 10)
>> -- residue 19884: duplicate [ O] atoms (total 10)
>> -- residue 19885: duplicate [ H1] atoms (total 10)
>> -- residue 19885: duplicate [ H2] atoms (total 10)
>> -- residue 19885: duplicate [ O] atoms (total 10)
>> -- residue 19886: duplicate [ H1] atoms (total 10)
>> -- residue 19886: duplicate [ H2] atoms (total 10)
>> -- residue 19886: duplicate [ O] atoms (total 10)
>> -- residue 19887: duplicate [ H1] atoms (total 10)
>> -- residue 19887: duplicate [ H2] atoms (total 10)
>> -- residue 19887: duplicate [ O] atoms (total 10)
>> -- residue 19888: duplicate [ H1] atoms (total 10)
>> -- residue 19888: duplicate [ H2] atoms (total 10)
>> -- residue 19888: duplicate [ O] atoms (total 10)
>> -- residue 19889: duplicate [ H1] atoms (total 10)
>> -- residue 19889: duplicate [ H2] atoms (total 10)
>> -- residue 19889: duplicate [ O] atoms (total 10)
>> -- residue 19890: duplicate [ H1] atoms (total 10)
>> -- residue 19890: duplicate [ H2] atoms (total 10)
>> -- residue 19890: duplicate [ O] atoms (total 10)
>> -- residue 19891: duplicate [ H1] atoms (total 10)
>> -- residue 19891: duplicate [ H2] atoms (total 10)
>> -- residue 19891: duplicate [ O] atoms (total 10)
>> -- residue 19892: duplicate [ H1] atoms (total 10)
>> -- residue 19892: duplicate [ H2] atoms (total 10)
>> -- residue 19892: duplicate [ O] atoms (total 10)
>> -- residue 19893: duplicate [ H1] atoms (total 10)
>> -- residue 19893: duplicate [ H2] atoms (total 10)
>> -- residue 19893: duplicate [ O] atoms (total 10)
>> -- residue 19894: duplicate [ H1] atoms (total 10)
>> -- residue 19894: duplicate [ H2] atoms (total 10)
>> -- residue 19894: duplicate [ O] atoms (total 10)
>> -- residue 19895: duplicate [ H1] atoms (total 10)
>> -- residue 19895: duplicate [ H2] atoms (total 10)
>> -- residue 19895: duplicate [ O] atoms (total 10)
>>
>> 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.)
>>
>> Matching PDB residue names to LEaP variables.
>> Starting new chain with Molecule
>> Starting new chain with Molecule
>> Starting new chain with Molecule
>> total atoms in file: 190868
>>
>> ******************************************************************
>>
>> Regarding the lipid residues, I always got these warnings referring to the split of them in three parts separated by the TER cards.
>>
>> With regard to the comment of Bill Ross, I verified that my pdb file follows the format of a standard one with the correct position of the digits. If I shift these positions, would I have errors/warnings in Leap?
>>
>> Anyway, I'll follow your suggestions related to the water molecules.
>>
>> Sincerely,
>>
>> Eduardo.
>>
>>
>>
>>
>>
>> ________________________________
>> De: Bill Ross <ross.cgl.ucsf.edu>
>> Enviado: sábado, 9 de janeiro de 2021 18:37
>> Para: amber.ambermd.org <amber.ambermd.org>
>> Assunto: Re: [AMBER] Error in xleap: water molecules
>>
>> I bet the res numbers are being chopped by reading the pdb format, and
>> maybe if they were shifted a position after the digits get too many
>> amber could handle them.
>>
>> Bill
>>
>> On 1/9/21 1:10 PM, David A Case wrote:
>>> On Sat, Jan 09, 2021, Eduardo R. Almeida wrote:
>>>> I used the symbol "..." to show that the file continues above and below the
>>>> snippet that I presented in this message.
>>> But can you show the *first* error or two?
>>>
>>> I'm thinking you will have to put the PDB into a Dropbox or equivalent.
>>> I've used tleap on an input pdb file that had 92,000 water molecules and
>>> about 1 million atoms. But packmol might be doing things that are odd with
>>> really big files (systems that are nominally too big for the PDB format).
>>>
>>> But what I would do is just what you could do as well: start by removing
>>> waters from the end of the file (if they are at the end) to see if you can
>>> get rid of the error. The put back just enough to trigger the error. This
>>> will localize the problem. (This is why I think it may help to report the
>>> first error you see.)
>>>
>>> ....dac
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sat Jan 09 2021 - 16:00:03 PST
