[gmx-users] Problems

Henrik Rundgren henrik at physc.su.se
Mon May 3 15:59:01 CEST 2004

Hello again. Yes I did change the number of entries at the top of the 
aminoacids.dat file. I figured that the simulation should run anyway and 
that there shouldn't be problems due to the fact that the topology was 
ok (looks like it). I added the combinations that wasn't made by 
pdb2gmx..... and started to simulate.. I have done EM and a couple of 
short MD's (2 X 10000 steps) to stabalize the box size and density 
a.s.o.... and to see that it works... and it did. I only collect the 
protein coords in the .XTC file, and it only records the atoms that are 
included as "Protein" Residues by Grompp.... I really must get grompp to 
understand that all atoms in the *.top should be included as 
"Protein".... I have tried to change name in the topology file, for 
instance from MELE to MELEU (I shortened the length of the res.names in 
*.pdb so that the "chain identifier" wouldn't go on)... but this didn't 
change the outcome.. so apparently grompp doesn't need to have the same 
names in *.top as in *.rtp files... Apparently it only cares that the 
residues are in aminoacids.dat to include that residue as a "Protein".. 
But this didn't work...

There is a problem when mdrun was ran, following error occured.. after about 81000 steps the following happened.
1.	Warning: 1-4 interaction at distance larger than 2.56
	These are ignored for the rest of the simulation
	turn on -debug for more information
	Segmentation fault

It's cyclic... atleast when I check the *.gro file.... and the short simulations ..... Maybe just something went baserk in it...
Does this segmentation fault have anything to do with the above mentioned problem? 

thanks for help/ideas in advance. henrik Message: 3 From: Marc Lensink 
<marc.lensink at ugent.be> Organization: University of Ghent To: 
gmx-users at gromacs.org Subject: Re: [gmx-users] Problem???!!? Date: Fri, 
30 Apr 2004 13:19:58 +0000 Reply-To: gmx-users at gromacs.org On Friday 30 
April 2004 12:38, Henrik Rundgren wrote:

>> Hi all.
>> I am doing a simulation on a cyclic peptide, with unusual a.a's.
>> They are included in the *.rtp file, and in aminoacids.dat a.s.o
>> But when I run grompp it will not report them to be a part of the
>> protein.. Only the "regular" residues are included as PROTEIN
>> residues, the rest to OTHER residues... WHY?

There's probably a file in the $GMXDATA/top/ directory that identifies
which residues are PROTEIN residues.

Change this file, or simply make an index file manually. I'd suggest
the latter.

The simulation will run fine, if your topology is okay.


Message: 4
Date: Fri, 30 Apr 2004 14:10:40 +0100
To: gmx-users at gromacs.org
From: Miguel Machuqueiro <machuque at itqb.unl.pt>
Subject: Re: [gmx-users] Problem???!!?
Reply-To: gmx-users at gromacs.org

At 13:38 30-04-2004, you wrote:

>>Hi all.
>>I am doing a simulation on a cyclic peptide, with unusual a.a's. They are 
>>included in the *.rtp file, and in aminoacids.dat a.s.o (...)
Did you update the total number of entries (first line) in the file 
aminoacids.dat??? I had the exact problem when I forgot to do so.

I did change the number of ebntrys at the top of the 

Henrik Rundgren
Division of Physical Chemistry
Arrhenius Laboratory
Stockholm University
S-106 91 Stockholm

E-mail:    Henrik at physc.su.se
Telephone: +46-(0)8-16 12 63
Fax:       +46-(0)8-15 21 87
Website:   www.fos.su.se/~henrik

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