Re: [gmx-users] 5-letter atom names in topology files

2017-06-23 Thread Qing Lv 



At 2017-06-23 21:55:39, "Justin Lemkul"  wrote:
>
>
>On 6/23/17 9:53 AM, Qing Lv wrote:
>> I tried pdb2gmx -merge interactive or -chainsep interactive, but neither 
>> work...
>
>There is no chain information in a .gro so this approach cannot work.  If you 
>have a multimeric complex, and you need to use these weird 5-character names, 
>process each .gro separately and merge the topologies manually (convert .top 
>-> 
>.itp and list them as #include statements in a new .top).



This is just what I have tried and succeeded eventually... Previously I made 
some mistakes when converting .top files to .itp.
Thanks.
Qing


>
>Or:
>
>1. Use a different force field that doesn't require format-breaking atom names.
>2. Change the names in the .rtp and coordinate file to preserve format 
>standards.
>
>-Justin
>
>-- 
>==
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
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>http://mackerell.umaryland.edu/~jalemkul
>
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Re: [gmx-users] 5-letter atom names in topology files

2017-06-23 Thread Justin Lemkul 



On 6/23/17 9:53 AM, Qing Lv wrote:

I tried pdb2gmx -merge interactive or -chainsep interactive, but neither work...


There is no chain information in a .gro so this approach cannot work.  If you 
have a multimeric complex, and you need to use these weird 5-character names, 
process each .gro separately and merge the topologies manually (convert .top -> 
.itp and list them as #include statements in a new .top).


Or:

1. Use a different force field that doesn't require format-breaking atom names.
2. Change the names in the .rtp and coordinate file to preserve format 
standards.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] 5-letter atom names in topology files

2017-06-23 Thread Qing Lv 
I tried pdb2gmx -merge interactive or -chainsep interactive, but neither work...
Qing


At 2017-06-23 17:19:55, "Fitsiou, Eleni"  wrote:
>Hi ,
>Rename your chains and you could use   -merge interactive and  the -ter flag
>Best 
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Re: [gmx-users] 5-letter atom names in topology files

2017-06-23 Thread Fitsiou, Eleni 
Hi ,
Rename your chains and you could use   -merge interactive and  the -ter flag
Best 
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Re: [gmx-users] 5-letter atom names in topology files

2017-06-23 Thread Qing Lv 
My protein contains 2 chains, and ILE294 is the C-terminus of chain 1. When I 
used pdb2gmx to process the GRO file, it can recognize N-terminus of chain 1 
and C-terminus of chain 2, but cannot recognize C-terminus of chain 1. Since 
there is no chain separators in GRO files (like "TER" in PDB), pdb2gmx might 
regard all aminoacids as one single chain.
Sorry for not having explained clearly in previous emails. Any suggestions?


Many thanks,
Qing


At 2017-06-23 16:24:13, "Qing Lv"  wrote:
>Dear Mark,
>
>
>Actually I had tried the method you suggested, but got such errors (pdb2gmx):
>Fatal error:
>Atom O1 in residue ILE 294 was not found in rtp entry ILE with 9 atoms while 
>sorting atoms.
>ILE294 is C-terminus of my protein. I looked up in aminoacids.rtp and there 
>are no atom "O1" or "O2" in ILE entry; however, I never got such errors when 
>using pdb2gmx to process PDB files. Maybe, pdb2gmx can only process terminal 
>residues for PDB files?
>
>
>Also, I have tried to process protein and ATP separately with pdb2gmx and then 
>combined them together, but met problems. That's why I sent another 2 emails...
>
>
>Qing
>
>
>At 2017-06-23 15:33:17, "Mark Abraham"  wrote:
>>Hi,
>>
>>I suggest you produce your initial conformation in .gro format, which
>>permits five-character atom names. That might mean using editconf on your
>>.pdb file, and then manually renaming atoms.
>>
>>Mark
>>
>>On Fri, Jun 23, 2017 at 3:55 AM Qing Lv  wrote:
>>
>>> Hi,
>>>
>>>
>>> Gromos 54a7 force field has built-in topologies for some small molecules,
>>> like ATP. In these topologies, many atoms have names of up to 5 letters,
>>> such as AO1PA and AO2PB. However, PDB files seem do not support 5-letter
>>> atom names. So, if I name an atom "AO2PB" in PDB, it will be truncated to
>>> "AO2P" or "O2PB" when executing pdb2gmx, and these atoms cannot be
>>> recognized then.
>>> Anyone know how to solvate this problem? Many thanks ^_^
>>>
>>>
>>> Qing
>>> --
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
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Re: [gmx-users] 5-letter atom names in topology files

2017-06-23 Thread Qing Lv 
Dear Mark,


Actually I had tried the method you suggested, but got such errors (pdb2gmx):
Fatal error:
Atom O1 in residue ILE 294 was not found in rtp entry ILE with 9 atoms while 
sorting atoms.
ILE294 is C-terminus of my protein. I looked up in aminoacids.rtp and there are 
no atom "O1" or "O2" in ILE entry; however, I never got such errors when using 
pdb2gmx to process PDB files. Maybe, pdb2gmx can only process terminal residues 
for PDB files?


Also, I have tried to process protein and ATP separately with pdb2gmx and then 
combined them together, but met problems. That's why I sent another 2 emails...


Qing


At 2017-06-23 15:33:17, "Mark Abraham"  wrote:
>Hi,
>
>I suggest you produce your initial conformation in .gro format, which
>permits five-character atom names. That might mean using editconf on your
>.pdb file, and then manually renaming atoms.
>
>Mark
>
>On Fri, Jun 23, 2017 at 3:55 AM Qing Lv  wrote:
>
>> Hi,
>>
>>
>> Gromos 54a7 force field has built-in topologies for some small molecules,
>> like ATP. In these topologies, many atoms have names of up to 5 letters,
>> such as AO1PA and AO2PB. However, PDB files seem do not support 5-letter
>> atom names. So, if I name an atom "AO2PB" in PDB, it will be truncated to
>> "AO2P" or "O2PB" when executing pdb2gmx, and these atoms cannot be
>> recognized then.
>> Anyone know how to solvate this problem? Many thanks ^_^
>>
>>
>> Qing
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
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>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
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Re: [gmx-users] 5-letter atom names in topology files

2017-06-23 Thread Mark Abraham 
Hi,

I suggest you produce your initial conformation in .gro format, which
permits five-character atom names. That might mean using editconf on your
.pdb file, and then manually renaming atoms.

Mark

On Fri, Jun 23, 2017 at 3:55 AM Qing Lv  wrote:

> Hi,
>
>
> Gromos 54a7 force field has built-in topologies for some small molecules,
> like ATP. In these topologies, many atoms have names of up to 5 letters,
> such as AO1PA and AO2PB. However, PDB files seem do not support 5-letter
> atom names. So, if I name an atom "AO2PB" in PDB, it will be truncated to
> "AO2P" or "O2PB" when executing pdb2gmx, and these atoms cannot be
> recognized then.
> Anyone know how to solvate this problem? Many thanks ^_^
>
>
> Qing
> --
> Gromacs Users mailing list
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[gmx-users] 5-letter atom names in topology files

2017-06-22 Thread Qing Lv 
Hi,


Gromos 54a7 force field has built-in topologies for some small molecules, like 
ATP. In these topologies, many atoms have names of up to 5 letters, such as 
AO1PA and AO2PB. However, PDB files seem do not support 5-letter atom names. 
So, if I name an atom "AO2PB" in PDB, it will be truncated to "AO2P" or "O2PB" 
when executing pdb2gmx, and these atoms cannot be recognized then.
Anyone know how to solvate this problem? Many thanks ^_^


Qing
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