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
--
Phobrain.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jan 09 2021 - 15:30:02 PST
