[gmx-users] OPLS to gromos96 problems

[Ken Rotondi]

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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