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
>>
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sat Jan 09 2021 - 16:00:02 PST
