Re: [gmx-users] missing atoms

[Mark Abraham]

swa...@ncbs.res.in wrote:

Hi All,

I am running Gromacs for drug enzyme complex using AMBER as
forcefield.While running pdb2gmx command I am getting error and warning of
790 missing atoms. Can anybody suggest me how to correct this error.


Either supply a structure file that has suitable hydrogens already built 
in with some external program, or see what the problem is with the AMBER 
.hdb file and your residues named CYSH. The required .hdb format is 
described in Chapter 5 of the manual.


Mark


error :
---
WARNING: atom H is missing in residue CYSH 703 in the pdb file
 You might need to add atom H to the hydrogen database of residue
CYSH
 in the file ff???.hdb (see the manual)


WARNING: atom HA is missing in residue CYSH 703 in the pdb file
 You might need to add atom HA to the hydrogen database of residue
CYSH
 in the file ff???.hdb (see the manual)


WARNING: atom HB1 is missing in residue CYSH 703 in the pdb file
 You might need to add atom HB1 to the hydrogen database of
residue CYSH
 in the file ff???.hdb (see the manual)


WARNING: atom HB2 is missing in residue CYSH 703 in the pdb file
 You might need to add atom HB2 to the hydrogen database of
residue CYSH
 in the file ff???.hdb (see the manual)

---
Program pdb2gmx_mpi, VERSION 3.3.1
Source code file: pdb2top.c, line: 697

Fatal error:
There were 790 missing atoms in molecule Protein_A, if you want to use
this incomplete topology anyhow, use the option -missing
---




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RE: [gmx-users] missing atoms

[Kukol, Andreas]

It is not straightforward to use the AMBER forcefield with Gromacs. You need to 
edit your pdb-file to account for different atom/residue names used by AMBER as 
opposed to GROMOS forcefields.
Detailed info is here: http://chemistry.csulb.edu/ffamber/

If this is your first MD simulation, try things with one of the Gromos 
forcefields first.

Andreas

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
> On Behalf Of swa...@ncbs.res.in
> Sent: 29 May 2009 10:21
> To: gmx-users@gromacs.org
> Subject: [gmx-users] missing atoms
>
> Hi All,
>
> I am running Gromacs for drug enzyme complex using AMBER as
> forcefield.While running pdb2gmx command I am getting error and warning of
> 790 missing atoms. Can anybody suggest me how to correct this error.
>
> error :
> ---
> WARNING: atom H is missing in residue CYSH 703 in the pdb file
>  You might need to add atom H to the hydrogen database of residue
> CYSH
>  in the file ff???.hdb (see the manual)
>
>
> WARNING: atom HA is missing in residue CYSH 703 in the pdb file
>  You might need to add atom HA to the hydrogen database of residue
> CYSH
>  in the file ff???.hdb (see the manual)
>
>
> WARNING: atom HB1 is missing in residue CYSH 703 in the pdb file
>  You might need to add atom HB1 to the hydrogen database of
> residue CYSH
>  in the file ff???.hdb (see the manual)
>
>
> WARNING: atom HB2 is missing in residue CYSH 703 in the pdb file
>  You might need to add atom HB2 to the hydrogen database of
> residue CYSH
>  in the file ff???.hdb (see the manual)
>
> ---
> Program pdb2gmx_mpi, VERSION 3.3.1
> Source code file: pdb2top.c, line: 697
>
> Fatal error:
> There were 790 missing atoms in molecule Protein_A, if you want to use
> this incomplete topology anyhow, use the option -missing
> ---
>
>
>
>
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[gmx-users] missing atoms

[swatik]

Hi All,

I am running Gromacs for drug enzyme complex using AMBER as
forcefield.While running pdb2gmx command I am getting error and warning of
790 missing atoms. Can anybody suggest me how to correct this error.

error :
---
WARNING: atom H is missing in residue CYSH 703 in the pdb file
 You might need to add atom H to the hydrogen database of residue
CYSH
 in the file ff???.hdb (see the manual)


WARNING: atom HA is missing in residue CYSH 703 in the pdb file
 You might need to add atom HA to the hydrogen database of residue
CYSH
 in the file ff???.hdb (see the manual)


WARNING: atom HB1 is missing in residue CYSH 703 in the pdb file
 You might need to add atom HB1 to the hydrogen database of
residue CYSH
 in the file ff???.hdb (see the manual)


WARNING: atom HB2 is missing in residue CYSH 703 in the pdb file
 You might need to add atom HB2 to the hydrogen database of
residue CYSH
 in the file ff???.hdb (see the manual)

---
Program pdb2gmx_mpi, VERSION 3.3.1
Source code file: pdb2top.c, line: 697

Fatal error:
There were 790 missing atoms in molecule Protein_A, if you want to use
this incomplete topology anyhow, use the option -missing
---




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Re: [gmx-users] missing atoms

[David van der Spoel]

ninoo mani wrote:

Dear gmx users
 
I have a protein molecule with few missing residues,

a Lys with CG, CD, CE, NZ missing atoms, and
a Val with CG1, CG2 missing atoms.
I noticed that pdb2gmx reads the pdb file and places the missing atoms.


Are you sure? I'm not aware of such a feature.

First I want to know whether gromacs places only missing atoms or it 
places the entire side chain?
Second, is gromacs' repaired molecule reliable for simulation or I 
should do homology modelling using other softwares to repair the molecule?

Thanks,
Ninoo


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--
David.

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se

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[gmx-users] missing atoms

[ninoo mani]

Dear gmx users     I have a protein molecule with few missing residues,  a Lys with CG, CD, CE, NZ missing atoms, and  a Val with CG1, CG2 missing atoms.  I noticed that pdb2gmx reads the pdb file and places the missing atoms.  First I want to know whether gromacs places only missing atoms or it places the entire side chain?   Second, is gromacs' repaired molecule reliable for simulation or I should do homology modelling using other softwares to repair the molecule?  Thanks,  Ninoo 
	

	
		 
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