Solvent.hdb Formatting Inquiry

User discussions
1

GROMACS version: 2020.22
GROMACS modification: Yes/No
Here post your question:

Hello is there anywhere where I may see some samples of solvent.hdb formatting?

My single water molecule pdb file only has the single O coordinates and is setting off a gmx pbd2gmx Fatal Error despite my -ignh within my command. I believe I must add these 2 hydrogens to my solvent.hdb file, however, could not find any samples how to do so successfully, any references on this would be appreciated, thanks:). ( I searched here and googled solvent.hdb etc. but could not discover a topic on this, if there is a different text search feel free to let me know.)

Below is my pdb coordinate file for the single HOH:

ATOM -1 O HOH Z -1 116.001 111.116 56.013 1.00 0.00 O
TER

Below is the exhibited Fatal Error:

Fatal error:
There were 2 missing atoms in molecule Water, if you want to use this
incomplete topology anyhow, use the option -missing

And below are some preceding text lines before the Fatal Error:

atom HW1 is missing in residue HOH -1 in the pdb file

atom HW1 is missing in residue HOH -1 in the pdb file

You might need to add atom HW1 to the hydrogen database of building block HOH in the file solvent.hdb (see the manual)

You might need to add atom HW1 to the hydrogen database of building block HOH in the file solvent.hdb (see the manual)

atom HW2 is missing in residue HOH -1 in the pdb file

atom HW2 is missing in residue HOH -1 in the pdb file

You might need to add atom HW2 to the hydrogen database of building block HOH in the file solvent.hdb (see the manual)

You might need to add atom HW2 to the hydrogen database of building block HOH in the file solvent.hdb (see the manual)

2

This is part of every standard force field within GROMACS (it’s in aminoacids.hdb):

HOH     1
2   7   HW  OW
3

Hi Justin thanks a bunch for the coding it executed successfully:).

4

Hi Justin,

I’m using GROMACS 2023 and charmm36-jul2022.ff, and I got the same errors about HW1 and HW2 atoms for each of the waters in the pdb I’m preparing. However, 1) there is no HOH entry in aminoacids.hdb in the July 2022 release, nor there is one in solvent.hdb. 2) Adding the HOH entry above to aminoacids.hdb did not fix the error, but adding it to solvent.hdb did. Is this something new in the 2022 port?

5

New, yes. Unintended, yes :)

The July 2022 port was produced with a totally new method so we’re still working out some things. CHARMM does not use HOH or SOL nomenclature, so we have to tell our program how to translate things, and I guess it’s not writing a corresponding .hdb entry when copying the TIP3 .rtp entry to SOL and HOH. There are no SOL or TIP3 .hdb entries, either. So we’ll have to work this out.

6

Thank you Justin! Does that mean there will be a 2023 port soon? ;)

7

I will do new releases when the CHARMM force field is updated, which occurs annually in July. Going forward, I will only release other versions when there are serious errors or omissions that need to be corrected, so an annual July port should be expected.

8

A related question about incorporating structural water molecules into the simulated system. How will they be treated when bulk solvent is added with gmx solvate? Will they get grouped with the added solvent waters, as a separate group of heterogens, or something else? Does this depend on whether the structural waters belong to a chain with a polypeptide or to a separate chain? (In my case I moved all structural waters to a chain of their own)

9

I haven’t worked with such a system in years, so I don’t know what the current behavior is. My recollection is that they do not get automatically merged, and that then potentially leads to headaches with discontinuous blocks of molecules requiring SETTLE, which isn’t supported.

10

Thank you! I will take this question to a separate thread for maximum exposure.

11

Hi Justin,
I’m using GROMACS 2021.4 and charmm36-jul2022.ff, and I got the same errors with TIP3 model from charmm-gui input generator. I have tried to add information to solvent.hdb but it did not fix the error:

You might need to add atom H1 to the hydrogen database of building block TIP3 in the file solvent.hdb (see the manual)

atom H2 is missing in residue TIP3 7727 in the pdb file

atom H2 is missing in residue TIP3 7727 in the pdb file

You might need to add atom H2 to the hydrogen database of building block TIP3 in the file solvent.hdb (see the manual)

You might need to add atom H2 to the hydrogen database of building block TIP3 in the file solvent.hdb (see the manual)

Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1534)

Fatal error:
There were 114570 missing atoms in molecule Other, if you want to use this
incomplete topology anyhow, use the option -missing

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation