Fwd: [gmx-users] add hydrogen atom in pdb file

[Justin A. Lemkul]

nafiseh farhadian wrote:
> 
> 
> 
> Dear Sir,
> thanks for your attention. i changed the force filed to ''ffgmx2'' and 
> ''ffG43a1'' but i receive a new fatal error abou ''atom type''.
>  
> for the next suggestion i addes ''ffgmx.hdb'' to the topology file but 
> there was alot of error as you see. what shall i do?
>  
> This is my topology file
> #define HEAVY_H
> ; Include forcefield parameters
> #include "ffgmx.itp"

Mark already told you not to use ffgmx.  If you think you're using ffG43a1, 
you're mistaken.

> ; Include hydrogen data bank
> #include "ffgmx.hdb"

What are you including an .hdb file in your topology?  It doesn't define 
parameters, and is only used by pdb2gmx and protonate in adding hydrogen atoms.

You have several other problems...see below.

> ; Include protein topology
> #include "top_A.itp"
> ; Include protein topology
> #include "top_B.itp"
> ; Include ibuprofen topology
> #include "ib.itp"
> ; Include water topology
> #include "spc.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
> ; Include generic topology for ions
> #include "ions.itp"
> [ system ]
> ; Name
> ibuprofen in HSA
> [ molecules ]
> ; Compound        #mols
> Protein_A            3
> Protein_B            0

Why are you including zero protein molecules?

> Na                   45

Na is not the appropriate name for the NA+ ion within ffG43a1 (have a look at 
ions.itp for the proper naming).

<snip>

> creating statusfile for 1 node...
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> WARNING 1 [file em.mdp, line unknown]:
>   Unknown left-hand 'bd-temp' in parameter file
> checking input for internal consistency...
> calling /lib/cpp...
> In file included from HSA.top:22:
> top_B.itp:35345:9: warning: no newline at end of file
> processing topology...
> ERROR 1 [file "/usr/local/gromacs/share/gromacs/top/ffgmx.hdb", line 1]:
>   *Incorrect number of atomtypes* for dihedral (1 instead of 2 or 4)
> ERROR 1 [file "/usr/local/gromacs/share/gromacs/top/ffgmx.hdb", line 2]:
>   Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
> ERROR 1 [file "/usr/local/gromacs/share/gromacs/top/ffgmx.hdb", line 3]:
>   Incorrect number of atomtypes for dihedral (1 instead of 2 or 4)
> ERROR 1 [file "/usr/local/gromacs/share/gromacs/top/ffgmx.hdb", line 4]:
>   Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
> .
> .
> .
> 
> ERROR 1 [file "/usr/local/gromacs/share/gromacs/top/ffgmx.hdb", line 146]:
>   Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
> Generated 1284 of the 1485 non-bonded parameter combinations

Deleting the #include "ffgmx.hdb" will eliminate all of these errors.

> WARNING 2 [file "top_B.itp", line 35345]:
>   Too few parameters on line (source file toppush.c, line 1168)
> Excluding 3 bonded neighbours for Protein_A 3
> Excluding 3 bonded neighbours for Protein_B 0
> Excluding 1 bonded neighbours for Na 45
> processing coordinates...
> -------------------------------------------------------
> Program grompp, VERSION 3.3.3
> Source code file: grompp.c, line: 469
> *Fatal error:
> number of coordinates in coordinate file (ucell-box.pdb, 18400)
>              does not match topology (HSA.top, 17574)
> *-------------------------------------------------------

This error could have any number of causes, probably due to your badly mangled 
topology.  It might be best to start over from pdb2gmx, using an appropriate 
force field.  I get the idea that you've already got a topology and you are 
trying to hack it to make it work with different force fields.  This is no easy 
task, and one should probably not do it.

-Justin

> 
>  
> On Sun, Dec 14, 2008 at 11:35 AM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 
>     nafiseh farhadian wrote:
> 
>         Dear Sir,
>         i'm one of the new gmx user. i have a problem with gromacs input
>         file.
>         i'll be thanking if you help me.
>          i'm working on protein system. i have pdb and itp file. in itp
>         file there are hydrogen atoms but in pdb file no. so when i
>         define top file the number of atoms don't match to each other
>         and i get a fattal error. my forcefield in top file is ''ffgmx
>         forcefield''. i'll be appriciate if you help me.
> 
> 
>     Don't use ffgmx for new simulations... it's been deprecated for
>     years, and pdb2gmx points this out.
> 
>     It's also always appropriate to cite the actual error message you
>     received, since if your interpretation of the problem was totally
>     reliable then you probably wouldn't need to be asking for help.
> 
>     You might try the protonate utility, or using pdb2gmx on your
>     structure to generate your .top file.
> 
>     Mark
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> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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