[gmx-users] OPLS to gromos96 problems

[Magnus Andersson]

HI again,

Sorry, answered the first part of your question...

/Magnus

> Hi Magnus,
>
> You were getting thousands of long bond warnings to a few crystal water?
>
> K
>
> On Jan 4, 2006, at 9:06 AM, Magnus Andersson wrote:
>
>> Hi,
>>
>> I encountered this problem some time ago. I had some xtal waters in the
>> .pdb file from which I removed the hydrogens (after getting that same
>> error message) and the pdb2gmx worked fine.
>>
>> /Magnus
>>
>>> Hello All,
>>>
>>> I've successfully built .gro and .top files for a large riboprotein in
>>> OPLSAA using GROMACS. The problem is that it is so large I really need
>>> to use a UAFF to keep this computationally tractable. I tried running
>>> pdb2gmx and received errors such as
>>>
>>> "WARNING: atom H21 is missing..."
>>>
>>> I entered the missing hydrogens to the .hdb file and fixed this.
>>> However this brought forth two additional problems:
>>>
>>> ----------------------------------------------------------------------
>>> --
>>> QUESTION 1) long bonds, there must be thousands
>>> eg
>>> Warning: Long Bond (74318-75599 = 13.2452 nm)
>>> Warning: Long Bond (74345-75599 = 13.5764 nm)
>>>
>>> Several questions: What do the atom numbers refer to? The input ".gro"
>>> file numbering? The uncompleted output .gro file? Also, I'd say with
>>> the exception of ~25 Long Bonds they are all between some atom and
>>> atom
>>> #75599. I find this confusing since I'm using a GROMACS .gro file as
>>> input. Are there any suggestions as to what this might mean?
>>>
>>> ----------------------------------------------------------------------
>>> --
>>> QUESTION 2) "Fatal error: Atom H211 not found in rtp database in
>>> residue GUA, it looks a bit like H21"
>>>
>>> I assume that this is due to the fact that I have >10,000 atoms in my
>>> system and the atom type and atom number columns are merging. GUA is
>>> the first nucleotide after 10,000 atoms and the atomtype and number
>>> appear thusly for the H21 atom in this residue:
>>>
>>> H2110013
>>>
>>> Is there a way to have GROMACS accept H21 rather than exiting? If this
>>> is not the case do I need to go back to the .pdb files to get around
>>> this problem?
>>>
>>> Many thanks, as always,
>>>
>>> Ken
>>>
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>>
>>
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