[gmx-users] Problems with pdb2gmx and grompp
Yang Ye
leafyoung81-group at yahoo.com
Fri May 5 04:00:23 CEST 2006
you shall have sections of
[ system ]
[ molecules ]
A 1
B ...
in the end of your top
Yang Ye
Eduardo Martins Lopes wrote:
> Greetings fellows, after i successfully installed the gromacs I had
> some success simulating simple systems but when it comes to a DPPC
> bilayer, i got the "old" DPP or DPPC residue not found in library.
>
> I did a deep research at the users list but none of the sugestions
> worked for me.
>
> To start playing around with Gromacs, I got the Prof. Tielman's
> DPPC.pdb, lipid.itp, dppc.itp, example2.top . I also got the benchmark
> files to try it out. Also got the modified ffG43a2x and every other
> modified force fields files I could find.
>
> Always having the very same problem using pdb2gmx (in order
> to generate the .ndx, .gro and .top files), it complained about not
> finding neither DPP nor DPPC in the residues library. To solve this
> problem I tried many things like:
>
> 1- I hacked the ffG43a2.itp inserting #include lipid.itp and dppc.itp
> but no improvements achieved
> 2 - Insert the lipid.itp data into ffG43a2.rtp file. The
> message changed to problem with .rtp file at line (nothing else)
> 3 - Removed the bad data of the .rtp file and then I modified the .hdb
> file but the message changed back to DPP (DPPC) residue not found in
> library
> 4 - I renamed the entire set of ffG43a2x files to ffG43a2 (backing up
> the old files) but the error messaged came back to the rtp. file problem.
>
> I found many many replies for this very same problem, but as I said,
> none of them could help me.
>
> After giving up on pdb2gmx, I went back to the benchmark files and
> tried to work with it (as I read on one of the list messages). I just
> modified the .top (DPPC 1) to fit my system. As you may noticed, i
> simplified my old system to 1 molecule.
>
> I had the same problem on pdb2gmx. But i went forward and tried
> to generate the .tpr file using grompp. This is the error:
> "Fatal error:
> number of coordinates in coordinate file
> (/home/debora/dppc/1dppcH.gro, 50)
> does not match topology (/home/debora/dppc/1dppcH.top, 0)"
>
> I went to http://davapc1.bioch.dundee.ac.uk/prodrg/ and inserted my
> pdb file there...I used the .gro, .top and the .pdb file (with H's)
> there and tried to generate the .tpr file...I got the sabe "not
> matching" error
> "Fatal error:
> number of coordinates in coordinate file
> (/home/debora/dppc/1dppcH.gro, 50)
> does not match topology (/home/debora/dppc/1dppcH.top, 0)"
>
> I really appreciate any hint on what should I do.
>
> Thanks in advance.
>
> Eduardo Martins Lopes
> Undergratuate Student at Universidade Federal de São Carlos UFSCar -
> SP Brazil
>
>
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