[gmx-users] Problems with pdb2gmx and grompp

[Yang Ye]

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 
>  
>
> ------------------------------------------------------------------------
> Abra sua conta no Yahoo! Mail 
> <http://us.rd.yahoo.com/mail/br/tagline/mail/*http://br.info.mail.yahoo.com/> 
> - 1GB de espaço, alertas de e-mail no celular e anti-spam realmente 
> eficaz.
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php